diff --git a/app/controllers/concerns/file_import_actions.rb b/app/controllers/concerns/file_import_actions.rb
index c7e416df9b..5b37370c5b 100644
--- a/app/controllers/concerns/file_import_actions.rb
+++ b/app/controllers/concerns/file_import_actions.rb
@@ -34,6 +34,6 @@ def create # rubocop:disable Metrics/AbcSize
   private
 
   def file_import_params
-    params.require(:file_import).permit(:file, :sample_id_column, :ignore_empty_values)
+    params.require(:file_import).permit(:file, :sample_id_column, :ignore_empty_values, metadata_columns: [])
   end
 end
diff --git a/app/javascript/controllers/metadata/file_import_controller.js b/app/javascript/controllers/metadata/file_import_controller.js
index 2abd75af52..f624058e63 100644
--- a/app/javascript/controllers/metadata/file_import_controller.js
+++ b/app/javascript/controllers/metadata/file_import_controller.js
@@ -2,11 +2,12 @@ import { Controller } from "@hotwired/stimulus";
 import * as XLSX from "xlsx";
 
 export default class extends Controller {
-  static targets = ["selectInput", "submitButton"];
+  static targets = ["sampleIdColumn", "metadataColumns", "submitButton"];
   static values = {
-    loaded: Boolean
+    loaded: Boolean,
   };
 
+  #headers = [];
   #disabled_classes = [
     "bg-slate-50",
     "border",
@@ -28,12 +29,26 @@ export default class extends Controller {
   ];
 
   connect() {
-    this.#disableSelectInput();
+    this.#disableTarget(this.sampleIdColumnTarget);
+    if (this.hasMetadataColumnsTarget) {
+      this.#disableTarget(this.metadataColumnsTarget);
+    }
     this.submitButtonTarget.disabled = true;
     this.loadedValue = true;
   }
 
-  toggleSubmitButton(event) {
+  changeSampleIDInput() {
+    if (this.hasMetadataColumnsTarget) {
+      this.#removeInputOptions(this.metadataColumnsTarget);
+      this.#addMetadataInputOptions();
+      this.#enableTarget(this.metadataColumnsTarget);
+      this.submitButtonTarget.disabled = true;
+    } else {
+      this.submitButtonTarget.disabled = false;
+    }
+  }
+
+  changeMetadataInput(event) {
     const { value } = event.target;
     this.submitButtonTarget.disabled = !value;
   }
@@ -42,7 +57,7 @@ export default class extends Controller {
     const { files } = event.target;
 
     if (!files.length) {
-      this.#removeSelectOptions();
+      this.#removeInputsOptions();
       return;
     }
 
@@ -53,33 +68,75 @@ export default class extends Controller {
       const workbook = XLSX.read(reader.result, { sheetRows: 1 });
       const worksheetName = workbook.SheetNames[0];
       const worksheet = workbook.Sheets[worksheetName];
-      const headers = XLSX.utils.sheet_to_json(worksheet, { header: 1 })[0];
-      this.#removeSelectOptions();
-      this.#addSelectOptions(headers);
+      this.#headers = XLSX.utils.sheet_to_json(worksheet, { header: 1 })[0];
+      this.#removeInputsOptions();
+      this.#addSampleIDInputOptions();
+      this.#enableTarget(this.sampleIdColumnTarget);
+      if (this.hasMetadataColumnsTarget) {
+        this.#disableTarget(this.metadataColumnsTarget);
+      }
     };
   }
 
-  #removeSelectOptions() {
-    while (this.selectInputTarget.options.length > 1) {
-      this.selectInputTarget.remove(this.selectInputTarget.options.length - 1);
+  #removeInputsOptions() {
+    this.#removeInputOptions(this.sampleIdColumnTarget);
+    this.#disableTarget(this.sampleIdColumnTarget);
+    if (this.hasMetadataColumnsTarget) {
+      this.#removeInputOptions(this.metadataColumnsTarget);
+      this.#disableTarget(this.metadataColumnsTarget);
     }
-    this.#disableSelectInput();
     this.submitButtonTarget.disabled = true;
   }
 
-  #addSelectOptions(headers) {
-    for (let header of headers) {
+  #addSampleIDInputOptions() {
+    for (let header of this.#headers) {
       const option = document.createElement("option");
       option.value = header;
       option.text = header;
-      this.selectInputTarget.append(option);
+      this.sampleIdColumnTarget.append(option);
     }
-    this.selectInputTarget.disabled = false;
-    this.selectInputTarget.classList.remove(...this.#disabled_classes);
   }
 
-  #disableSelectInput() {
-    this.selectInputTarget.disabled = true;
-    this.selectInputTarget.classList.add(...this.#disabled_classes);
+  #addMetadataInputOptions() {
+    const ignoreList = [
+      "sample id",
+      "sample name",
+      "project id",
+      "created_at",
+      "updated_at",
+      "last_updated_at",
+    ];
+
+    let columns = this.#headers.filter(
+      (header) =>
+        !ignoreList.includes(header.toLowerCase()) &&
+        header.toLowerCase() != this.sampleIdColumnTarget.value.toLowerCase(),
+    );
+
+    for (let column of columns) {
+      const option = document.createElement("option");
+      option.value = column;
+      option.text = column;
+      this.metadataColumnsTarget.append(option);
+    }
+  }
+
+  #removeInputOptions(target) {
+    for (let index = target.options.length - 1; index >= 0; index--) {
+      //do not remove the placeholder
+      if (target.options[index].value) {
+        target.remove(index);
+      }
+    }
+  }
+
+  #disableTarget(target) {
+    target.disabled = true;
+    target.classList.add(...this.#disabled_classes);
+  }
+
+  #enableTarget(target) {
+    target.disabled = false;
+    target.classList.remove(...this.#disabled_classes);
   }
 }
diff --git a/app/services/samples/metadata/file_import_service.rb b/app/services/samples/metadata/file_import_service.rb
index 7e8e321950..e10aec21e9 100644
--- a/app/services/samples/metadata/file_import_service.rb
+++ b/app/services/samples/metadata/file_import_service.rb
@@ -8,9 +8,9 @@ module Metadata
     class FileImportService < BaseSpreadsheetImportService
       def initialize(namespace, user = nil, blob_id = nil, params = {})
         @sample_id_column = params[:sample_id_column]
-        required_headers = [@sample_id_column]
+        @selected_headers = params[:metadata_columns] || []
         @ignore_empty_values = params[:ignore_empty_values]
-        super(namespace, user, blob_id, required_headers, 1, params)
+        super(namespace, user, blob_id, [@sample_id_column], 1, params)
       end
 
       def execute
@@ -24,9 +24,14 @@ def execute
 
       protected
 
-      def perform_file_import
+      def perform_file_import # rubocop:disable Metrics/MethodLength
         response = {}
-        parse_settings = @headers.zip(@headers).to_h
+        headers = if Flipper.enabled?(:metadata_import_field_selection)
+                    @selected_headers << @sample_id_column
+                  else
+                    @headers
+                  end
+        parse_settings = headers.zip(headers).to_h
         @spreadsheet.each_with_index(parse_settings) do |metadata, index|
           next unless index.positive?
 
diff --git a/app/views/shared/samples/metadata/file_imports/_dialog.html.erb b/app/views/shared/samples/metadata/file_imports/_dialog.html.erb
index b8973cfc35..9f1032b9ce 100644
--- a/app/views/shared/samples/metadata/file_imports/_dialog.html.erb
+++ b/app/views/shared/samples/metadata/file_imports/_dialog.html.erb
@@ -47,10 +47,26 @@
                         { prompt: t(".select_sample_id_column") },
                         required: true,
                         data: {
-                          "metadata--file-import-target": "selectInput",
-                          action: "change->metadata--file-import#toggleSubmitButton",
+                          "metadata--file-import-target": "sampleIdColumn",
+                          action: "change->metadata--file-import#changeSampleIDInput",
                         } %>
           </div>
+          <% if Flipper.enabled?(:metadata_import_field_selection) %>
+            <div class="form-field">
+              <%= form.label :metadata_columns,
+                         t(".metadata_columns"),
+                         class:
+                           "block mb-2 text-sm font-medium text-slate-900 dark:text-white" %>
+              <%= form.select :metadata_columns,
+                          {},
+                          { multiple: true, include_hidden: false },
+                          required: true,
+                          data: {
+                            "metadata--file-import-target": "metadataColumns",
+                            action: "change->metadata--file-import#changeMetadataInput",
+                          } %>
+            </div>
+          <% end %>
           <div class="flex items-center">
             <%= form.check_box :ignore_empty_values,
                            {
diff --git a/config/locales/en.yml b/config/locales/en.yml
index df2ecba18d..415e6ce428 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1819,8 +1819,9 @@ en:
             file_help: CSV, TSV, XLS or XLSX.
             ignore_empty_values:
               description: If selected, any metadata fields without an associated value will be ignored and those metadata keys will not be removed from the sample if present. However, if this not selected, any samples with the metadata key and empty value will be deleted.
+            metadata_columns: Metadata Columns
             namespace:
-              description: 'The spreadsheet is required to have a column that contains a sample identifier. '
+              description: The spreadsheet is required to have a column that contains a sample identifier.
               group:
                 description_html: The identifier is case-sensitive and must contain the <b>sample ID</b>.
               project:
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index ea6f7d4dc4..61db93549b 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1819,8 +1819,9 @@ fr:
             file_help: CSV, TSV, XLS or XLSX.
             ignore_empty_values:
               description: If selected, any metadata fields without an associated value will be ignored and those metadata keys will not be removed from the sample if present. However, if this not selected, any samples with the metadata key and empty value will be deleted.
+            metadata_columns: Metadata Columns
             namespace:
-              description: 'The spreadsheet is required to have a column that contains a sample identifier. '
+              description: The spreadsheet is required to have a column that contains a sample identifier.
               group:
                 description_html: The identifier is case-sensitive and must contain the <b>sample ID</b>.
               project:
diff --git a/db/seeds.rb b/db/seeds.rb
index e246bc1c8a..1c761269aa 100644
--- a/db/seeds.rb
+++ b/db/seeds.rb
@@ -5,6 +5,7 @@
 Faker::Config.locale = 'en'
 
 Flipper.enable(:workflow_execution_sharing)
+Flipper.enable(:metadata_import_field_selection)
 
 @namespace_group_link_expiry_date = (Time.zone.today + 14).strftime('%Y-%m-%d')
 
diff --git a/docs-site/docs/extend/grapgql_sample_filter.md b/docs-site/docs/extend/graphql_sample_filter.md
similarity index 100%
rename from docs-site/docs/extend/grapgql_sample_filter.md
rename to docs-site/docs/extend/graphql_sample_filter.md
diff --git a/test/fixtures/files/metadata/duplicate_headers.csv b/test/fixtures/files/metadata/duplicate_headers.csv
index c7b2dfc6f1..fa5bef3539 100644
--- a/test/fixtures/files/metadata/duplicate_headers.csv
+++ b/test/fixtures/files/metadata/duplicate_headers.csv
@@ -1,3 +1,3 @@
-sample_name,metadatafield1,metadatafield2,sample_name,metadatafield3
-Project 1 Sample 1,10,20,Project 1 Sample 1,30
-Project 1 Sample 2,15,25,Project 1 Sample 2,35
+sample_name,metadatafield1,metadatafield2,metadatafield3,metadatafield3
+Project 1 Sample 1,10,20,30,30
+Project 1 Sample 2,15,25,35,35
diff --git a/test/fixtures/files/metadata/invalid.txt b/test/fixtures/files/metadata/invalid.txt
index addbfb8ede..afca8bc76b 100644
--- a/test/fixtures/files/metadata/invalid.txt
+++ b/test/fixtures/files/metadata/invalid.txt
@@ -1 +1 @@
-invalid file extension
+invalid file extension,header
diff --git a/test/services/samples/metadata/file_import_service_test.rb b/test/services/samples/metadata/file_import_service_test.rb
index 4534147b0f..4051ed3408 100644
--- a/test/services/samples/metadata/file_import_service_test.rb
+++ b/test/services/samples/metadata/file_import_service_test.rb
@@ -6,6 +6,8 @@ module Samples
   module Metadata
     class FileImportServiceTest < ActiveSupport::TestCase
       def setup
+        Flipper.enable(:metadata_import_field_selection)
+
         @john_doe = users(:john_doe)
         @jane_doe = users(:jane_doe)
         @group = groups(:group_one)
@@ -79,7 +81,7 @@ def setup
       test 'import sample metadata via csv file using sample names for project namespace' do
         assert_equal({}, @sample1.metadata)
         assert_equal({}, @sample2.metadata)
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, @blob.id,
                                                             params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
@@ -104,7 +106,7 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_puid' }
+        params = { sample_id_column: 'sample_puid', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.puid => { added: %w[metadatafield1 metadatafield2 metadatafield3],
@@ -142,7 +144,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_puid' }
+        params = { sample_id_column: 'sample_puid',
+                   metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@group, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.puid => { added: %w[metadatafield1 metadatafield2 metadatafield3],
@@ -167,7 +170,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name',
+                   metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id, params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] },
@@ -192,7 +196,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name',
+                   metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id, params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] },
@@ -216,7 +221,7 @@ def setup
           filename: file.original_filename,
           content_type: file.content_type
         )
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
@@ -320,7 +325,7 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield3],
@@ -343,7 +348,7 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield3],
@@ -367,7 +372,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name', ignore_empty_values: true }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3],
+                   ignore_empty_values: true }
         response = Samples::Metadata::FileImportService.new(project29.namespace, @john_doe, blob.id, params).execute
         assert_equal({ sample32.name => { added: ['metadatafield3'], updated: ['metadatafield2'],
                                           deleted: [], not_updated: [], unchanged: [] } }, response)
@@ -394,7 +400,7 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(project31.namespace, @john_doe, blob.id, params).execute
         assert_empty response
         assert_equal("Sample 'Sample 34' with field(s) 'metadatafield1' cannot be updated.",
@@ -416,7 +422,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name', ignore_empty_values: false }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3],
+                   ignore_empty_values: false }
         response = Samples::Metadata::FileImportService.new(project29.namespace, @john_doe, blob.id, params).execute
         assert_equal({ sample32.name => { added: ['metadatafield3'], updated: ['metadatafield2'],
                                           deleted: ['metadatafield1'], not_updated: [], unchanged: [] } }, response)
@@ -437,7 +444,8 @@ def setup
           content_type: file.content_type
         )
 
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name',
+                   metadata_columns: ['sample_name', 'metadatafield1', ' metadatafield2 ', 'metadatafield3'] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id,
                                                             params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
@@ -461,7 +469,7 @@ def setup
           filename: file.original_filename,
           content_type: file.content_type
         )
-        params = { sample_id_column: 'sample_name' }
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1 metadatafield2 metadatafield3] }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, blob.id, params).execute
         assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] } }, response)
@@ -475,6 +483,22 @@ def setup
                      @sample1.reload.metadata)
         assert_equal({}, @sample2.reload.metadata)
       end
+
+      test 'import sample metadata selecting a column' do
+        assert_equal({}, @sample1.metadata)
+        assert_equal({}, @sample2.metadata)
+        params = { sample_id_column: 'sample_name', metadata_columns: %w[metadatafield1] }
+        response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, @blob.id,
+                                                            params).execute
+        assert_equal({ @sample1.name => { added: %w[metadatafield1],
+                                          updated: [], deleted: [], not_updated: [], unchanged: [] },
+                       @sample2.name => { added: %w[metadatafield1],
+                                          updated: [], deleted: [], not_updated: [], unchanged: [] } }, response)
+        assert_equal({ 'metadatafield1' => '10' },
+                     @sample1.reload.metadata)
+        assert_equal({ 'metadatafield1' => '15' },
+                     @sample2.reload.metadata)
+      end
     end
   end
 end
diff --git a/test/system/groups/samples_test.rb b/test/system/groups/samples_test.rb
index 59485d457a..4d74b45dbc 100644
--- a/test/system/groups/samples_test.rb
+++ b/test/system/groups/samples_test.rb
@@ -7,6 +7,8 @@ class SamplesTest < ApplicationSystemTestCase
     include ActionView::Helpers::SanitizeHelper
 
     def setup
+      Flipper.enable(:metadata_import_field_selection)
+
       @user = users(:john_doe)
       login_as @user
       @group = groups(:group_one)
@@ -793,6 +795,9 @@ def retrieve_puids
       within('div[data-metadata--file-import-loaded-value="true"]') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/valid_with_puid.csv')
         find('#file_import_sample_id_column', wait: 1).find("option[value='sample_puid']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
@@ -811,12 +816,11 @@ def retrieve_puids
       within('div[data-metadata--file-import-loaded-value="true"]') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/invalid.txt')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='header']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
-      end
-      assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
-
-      perform_enqueued_jobs only: [::Samples::MetadataImportJob]
 
+        perform_enqueued_jobs only: [::Samples::MetadataImportJob]
+      end
       within %(turbo-frame[id="samples_dialog"]) do
         assert_text I18n.t('services.spreadsheet_import.invalid_file_extension')
       end
@@ -832,6 +836,9 @@ def retrieve_puids
         attach_file 'file_import[file]',
                     Rails.root.join('test/fixtures/files/metadata/contains_empty_values_with_puid.csv')
         find('#file_import_sample_id_column', wait: 1).find("option[value='sample_puid']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         check 'Ignore empty values'
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
@@ -868,6 +875,9 @@ def retrieve_puids
         attach_file 'file_import[file]',
                     Rails.root.join('test/fixtures/files/metadata/contains_empty_values_with_puid.csv')
         find('#file_import_sample_id_column', wait: 1).find("option[value='sample_puid']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         assert_not find_field('Ignore empty values').checked?
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
@@ -895,6 +905,10 @@ def retrieve_puids
       within('div[data-metadata--file-import-loaded-value="true"]') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/duplicate_headers.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[1]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[3]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[4]').select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
@@ -912,6 +926,9 @@ def retrieve_puids
       within('div[data-metadata--file-import-loaded-value="true"]') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/missing_metadata_rows.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
@@ -929,14 +946,7 @@ def retrieve_puids
       within('div[data-metadata--file-import-loaded-value="true"]') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/missing_metadata_columns.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
-        click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
-      end
-      assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
-
-      perform_enqueued_jobs only: [::Samples::MetadataImportJob]
-
-      within %(turbo-frame[id="samples_dialog"]) do
-        assert_text I18n.t('services.spreadsheet_import.missing_data_columns')
+        assert find("input[value='#{I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')}'").disabled?
       end
     end
 
@@ -955,6 +965,9 @@ def retrieve_puids
         attach_file 'file_import[file]',
                     Rails.root.join('test/fixtures/files/metadata/mixed_project_samples_with_puid.csv')
         find('#file_import_sample_id_column', wait: 1).find("option[value='sample_puid']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
@@ -976,6 +989,8 @@ def retrieve_puids
         attach_file 'file_import[file]',
                     Rails.root.join('test/fixtures/files/metadata/contains_analysis_values_with_puid.csv')
         find('#file_import_sample_id_column', wait: 1).find("option[value='sample_puid']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
diff --git a/test/system/projects/samples_test.rb b/test/system/projects/samples_test.rb
index 4f9ca3997e..9d1a9c2748 100644
--- a/test/system/projects/samples_test.rb
+++ b/test/system/projects/samples_test.rb
@@ -7,6 +7,8 @@ class SamplesTest < ApplicationSystemTestCase
     include ActionView::Helpers::SanitizeHelper
 
     setup do
+      Flipper.enable(:metadata_import_field_selection)
+
       @user = users(:john_doe)
       login_as @user
       @sample1 = samples(:sample1)
@@ -1171,6 +1173,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/valid.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
         ### ACTIONS END ###
       end
@@ -1247,6 +1252,10 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/valid.xls')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield4']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###
@@ -1323,6 +1332,10 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/valid.xlsx')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield4']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
         ### ACTIONS END ###
       end
@@ -1374,6 +1387,7 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/invalid.txt')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='header']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###
@@ -1415,6 +1429,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/contains_empty_values.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         # enable ignore empty values
         find('input#file_import_ignore_empty_values').click
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
@@ -1465,6 +1482,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/contains_empty_values.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         # leave ignore empty values disabled
         assert_not find('input#file_import_ignore_empty_values').checked?
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
@@ -1499,6 +1519,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/duplicate_headers.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[1]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find(:xpath, 'option[3]').select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###
@@ -1526,6 +1549,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/missing_metadata_rows.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###
@@ -1553,18 +1579,12 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/missing_metadata_columns.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
-        click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
-      end
-      ### ACTIONS END ###
-
-      ### VERIFY START ###
-      assert_text I18n.t('shared.samples.metadata.file_imports.dialog.spinner_message')
-
-      perform_enqueued_jobs only: [::Samples::MetadataImportJob]
+        ### ACTIONS END ###
 
-      # error msg
-      assert_text I18n.t('services.spreadsheet_import.missing_data_columns')
-      ### VERIFY END ###
+        ### VERIFY START ###
+        assert find("input[value='#{I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')}'").disabled?
+        ### VERIFY END ###
+      end
     end
 
     test 'should partially import metadata with missing sample errors' do
@@ -1599,6 +1619,9 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/mixed_project_samples.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield2']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###
@@ -1658,6 +1681,8 @@ class SamplesTest < ApplicationSystemTestCase
       within('#dialog') do
         attach_file 'file_import[file]', Rails.root.join('test/fixtures/files/metadata/contains_analysis_values.csv')
         find('#file_import_sample_id_column', wait: 1).find(:xpath, 'option[2]').select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield1']").select_option
+        find('#file_import_metadata_columns', wait: 1).find("option[value='metadatafield3']").select_option
         click_on I18n.t('shared.samples.metadata.file_imports.dialog.submit_button')
       end
       ### ACTIONS END ###