diff --git a/changelogs/client_server/newsfragments/2051.clarification b/changelogs/client_server/newsfragments/2051.clarification
new file mode 100644
index 000000000..e8f7a70c7
--- /dev/null
+++ b/changelogs/client_server/newsfragments/2051.clarification
@@ -0,0 +1,2 @@
+Document the `instance_id` field of `Protocol Instance` in the responses to
+`GET /_matrix/client/v3/thirdparty/protocols` and `GET /_matrix/client/v3/thirdparty/protocol/{protocol}`.
diff --git a/data/api/application-service/definitions/protocol.yaml b/data/api/application-service/definitions/protocol.yaml
index ff6300dbd..eb56ab26b 100644
--- a/data/api/application-service/definitions/protocol.yaml
+++ b/data/api/application-service/definitions/protocol.yaml
@@ -11,101 +11,15 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-title: Protocol
-type: object
-properties:
-  user_fields:
-    description: |-
-      Fields which may be used to identify a third-party user. These should be
-      ordered to suggest the way that entities may be grouped, where higher
-      groupings are ordered first. For example, the name of a network should be
-      searched before the nickname of a user.
-    type: array
-    items:
-      type: string
-      description: Field used to identify a third-party user.
-    example: ["network", "nickname"]
-  location_fields:
-    description: |-
-      Fields which may be used to identify a third-party location. These should be
-      ordered to suggest the way that entities may be grouped, where higher
-      groupings are ordered first. For example, the name of a network should be
-      searched before the name of a channel.
-    type: array
-    items:
-      type: string
-      description: Field used to identify a third-party location.
-    example: ["network", "channel"]
-  icon:
-    description: A content URI representing an icon for the third-party protocol.
-    type: string
-    example: "mxc://example.org/aBcDeFgH"
-  field_types:
-    description: |-
-      The type definitions for the fields defined in `user_fields` and
-      `location_fields`. Each entry in those arrays MUST have an entry here.
-      The `string` key for this object is the field name itself.
-
-      May be an empty object if no fields are defined.
-    type: object
-    additionalProperties:
-      title: Field Type
-      description: Definition of valid values for a field.
-      type: object
-      properties:
-        regexp:
-          description: |-
-            A regular expression for validation of a field's value. This may be relatively
-            coarse to verify the value as the application service providing this protocol
-            may apply additional validation or filtering.
-          type: string
-        placeholder:
-          description: A placeholder serving as a valid example of the field value.
-          type: string
-      required: ['regexp', 'placeholder']
-    example: {
-      "network": {
-        "regexp": "([a-z0-9]+\\.)*[a-z0-9]+",
-        "placeholder": "irc.example.org"
-      },
-      "nickname": {
-        "regexp": "[^\\s#]+",
-        "placeholder": "username"
-      },
-      "channel": {
-        "regexp": "#[^\\s]+",
-        "placeholder": "#foobar"
-      }
-    }
-  instances:
-    description: |-
-      A list of objects representing independent instances of configuration.
-      For example, multiple networks on IRC if multiple are provided by the
-      same application service.
-    type: array
-    items:
-      type: object
-      title: Protocol Instance
-      properties:
-        desc:
-          type: string
-          description: A human-readable description for the protocol, such as the name.
-          example: "Freenode"
-        icon:
-          type: string
-          description: |-
-            An optional content URI representing the protocol. Overrides the one provided
-            at the higher level Protocol object.
-          example: "mxc://example.org/JkLmNoPq"
-        fields:
-          type: object
-          description: Preset values for `fields` the client may use to search by.
-          example: {
-            "network": "freenode"
-          }
-        network_id:
-          type: string
-          description: A unique identifier across all instances.
-          example: "freenode"
-      required: ['desc', 'fields', 'network_id']
-required: ['user_fields', 'location_fields', 'icon', 'field_types', 'instances']
+allOf:
+- $ref: protocol_base.yaml
+- type: object
+  properties:
+    instances:
+      description: |-
+        A list of objects representing independent instances of configuration.
+        For example, multiple networks on IRC if multiple are provided by the
+        same application service.
+      type: array
+      items:
+        $ref: protocol_instance.yaml
diff --git a/data/api/application-service/definitions/protocol_base.yaml b/data/api/application-service/definitions/protocol_base.yaml
new file mode 100644
index 000000000..0238104fb
--- /dev/null
+++ b/data/api/application-service/definitions/protocol_base.yaml
@@ -0,0 +1,80 @@
+# Copyright 2018 New Vector Ltd
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+title: Protocol
+type: object
+properties:
+  user_fields:
+    description: |-
+      Fields which may be used to identify a third-party user. These should be
+      ordered to suggest the way that entities may be grouped, where higher
+      groupings are ordered first. For example, the name of a network should be
+      searched before the nickname of a user.
+    type: array
+    items:
+      type: string
+      description: Field used to identify a third-party user.
+    example: ["network", "nickname"]
+  location_fields:
+    description: |-
+      Fields which may be used to identify a third-party location. These should be
+      ordered to suggest the way that entities may be grouped, where higher
+      groupings are ordered first. For example, the name of a network should be
+      searched before the name of a channel.
+    type: array
+    items:
+      type: string
+      description: Field used to identify a third-party location.
+    example: ["network", "channel"]
+  icon:
+    description: A content URI representing an icon for the third-party protocol.
+    type: string
+    example: "mxc://example.org/aBcDeFgH"
+  field_types:
+    description: |-
+      The type definitions for the fields defined in `user_fields` and
+      `location_fields`. Each entry in those arrays MUST have an entry here.
+      The `string` key for this object is the field name itself.
+
+      May be an empty object if no fields are defined.
+    type: object
+    additionalProperties:
+      title: Field Type
+      description: Definition of valid values for a field.
+      type: object
+      properties:
+        regexp:
+          description: |-
+            A regular expression for validation of a field's value. This may be relatively
+            coarse to verify the value as the application service providing this protocol
+            may apply additional validation or filtering.
+          type: string
+        placeholder:
+          description: A placeholder serving as a valid example of the field value.
+          type: string
+      required: ['regexp', 'placeholder']
+    example: {
+      "network": {
+        "regexp": "([a-z0-9]+\\.)*[a-z0-9]+",
+        "placeholder": "irc.example.org"
+      },
+      "nickname": {
+        "regexp": "[^\\s#]+",
+        "placeholder": "username"
+      },
+      "channel": {
+        "regexp": "#[^\\s]+",
+        "placeholder": "#foobar"
+      }
+    }
+required: ['user_fields', 'location_fields', 'icon', 'field_types', 'instances']
diff --git a/data/api/application-service/definitions/protocol_instance.yaml b/data/api/application-service/definitions/protocol_instance.yaml
new file mode 100644
index 000000000..ef8f25661
--- /dev/null
+++ b/data/api/application-service/definitions/protocol_instance.yaml
@@ -0,0 +1,37 @@
+# Copyright 2018 New Vector Ltd
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+type: object
+title: Protocol Instance
+properties:
+  desc:
+    type: string
+    description: A human-readable description for the protocol, such as the name.
+    example: "Freenode"
+  icon:
+    type: string
+    description: |-
+      An optional content URI representing the protocol. Overrides the one provided
+      at the higher level Protocol object.
+    example: "mxc://example.org/JkLmNoPq"
+  fields:
+    type: object
+    description: Preset values for `fields` the client may use to search by.
+    example: {
+      "network": "freenode"
+    }
+  network_id:
+    type: string
+    description: A unique identifier across all instances.
+    example: "freenode"
+required: ['desc', 'fields', 'network_id']
diff --git a/data/api/application-service/definitions/protocol_metadata.yaml b/data/api/application-service/definitions/protocol_metadata.yaml
deleted file mode 100644
index cd2af89f2..000000000
--- a/data/api/application-service/definitions/protocol_metadata.yaml
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 2018 New Vector Ltd
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-type: object
-description: Dictionary of supported third-party protocols.
-additionalProperties:
-  $ref: protocol.yaml
-example: {
-  "irc": {
-    "user_fields": ["network", "nickname"],
-    "location_fields": ["network", "channel"],
-    "icon": "mxc://example.org/aBcDeFgH",
-    "field_types": {
-      "network": {
-        "regexp": "([a-z0-9]+\\.)*[a-z0-9]+",
-        "placeholder": "irc.example.org"
-      },
-      "nickname": {
-        "regexp": "[^\\s]+",
-        "placeholder": "username"
-      },
-      "channel": {
-        "regexp": "#[^\\s]+",
-        "placeholder": "#foobar"
-      }
-    },
-    "instances": [
-      {
-        "network_id": "freenode",
-        "desc": "Freenode",
-        "icon": "mxc://example.org/JkLmNoPq",
-        "fields": {
-          "network": "freenode.net",
-        }
-      }
-    ]
-  },
-  "gitter": {
-    "user_fields": ["username"],
-    "location_fields": ["room"],
-    "field_types": {
-      "username": {
-        "regexp": "@[^\\s]+",
-        "placeholder": "@username"
-      },
-      "room": {
-        "regexp": "[^\\s]+\\/[^\\s]+",
-        "placeholder": "matrix-org/matrix-doc"
-      }
-    },
-    "instances": [
-      {
-        "network_id": "gitter",
-        "desc": "Gitter",
-        "icon": "mxc://example.org/zXyWvUt",
-        "fields": {}
-      }
-    ]
-  }
-}
\ No newline at end of file
diff --git a/data/api/client-server/definitions/protocol.yaml b/data/api/client-server/definitions/protocol.yaml
new file mode 100644
index 000000000..96db7736d
--- /dev/null
+++ b/data/api/client-server/definitions/protocol.yaml
@@ -0,0 +1,43 @@
+# Copyright 2018 New Vector Ltd
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+allOf:
+- $ref: ../../application-service/definitions/protocol_base.yaml
+- type: object
+  properties:
+    instances:
+      description: |-
+        A list of objects representing independent instances of configuration.
+        For example, multiple networks on IRC if multiple are provided by the
+        same application service.
+
+        The instances are modified by the homeserver from the response of
+        [`GET /_matrix/app/v1/thirdparty/protocol/{protocol}`](/application-service-api/#get_matrixappv1thirdpartyprotocolprotocol)
+        to include an `instance_id` to serve as a unique identifier for each
+        instance on the homeserver.
+      type: array
+      items:
+        allOf:
+          - $ref: ../../application-service/definitions/protocol_instance.yaml
+          - type: object
+            properties:
+              instance_id:
+                type: string
+                description: |-
+                  A unique identifier for this instance on the homeserver. This field is added
+                  to the response of [`GET /_matrix/app/v1/thirdparty/protocol/{protocol}`](/application-service-api/#get_matrixappv1thirdpartyprotocolprotocol)
+                  by the homeserver.
+                  
+                  This is the identifier to use as the `third_party_instance_id` in a request to
+                  [`POST /_matrix/client/v3/publicRooms`](/client-server-api/#post_matrixclientv3publicrooms).
+                example: "irc-freenode"
diff --git a/data/api/client-server/list_public_rooms.yaml b/data/api/client-server/list_public_rooms.yaml
index 497ccb443..ffd202a48 100644
--- a/data/api/client-server/list_public_rooms.yaml
+++ b/data/api/client-server/list_public_rooms.yaml
@@ -233,6 +233,9 @@ paths:
                   description: |-
                     The specific third-party network/protocol to request from the
                     homeserver. Can only be used if `include_all_networks` is false.
+
+                    This is the `instance_id` of a `Protocol Instance` returned by
+                    [`GET /_matrix/client/v3/thirdparty/protocols`](/client-server-api/#get_matrixclientv3thirdpartyprotocols).
                   example: irc
               example: {
                 "limit": 10,
@@ -244,7 +247,7 @@ paths:
                   ]
                 },
                 "include_all_networks": false,
-                "third_party_instance_id": "irc"
+                "third_party_instance_id": "irc-freenode"
               }
         description: Options for which rooms to return.
         required: true
diff --git a/data/api/client-server/third_party_lookup.yaml b/data/api/client-server/third_party_lookup.yaml
index 3055b8aec..152f277de 100644
--- a/data/api/client-server/third_party_lookup.yaml
+++ b/data/api/client-server/third_party_lookup.yaml
@@ -33,7 +33,65 @@ paths:
           content:
             application/json:
               schema:
-                $ref: ../application-service/definitions/protocol_metadata.yaml
+                type: object
+                description: Dictionary of supported third-party protocols.
+                additionalProperties:
+                  $ref: definitions/protocol.yaml
+                example: {
+                  "irc": {
+                    "user_fields": ["network", "nickname"],
+                    "location_fields": ["network", "channel"],
+                    "icon": "mxc://example.org/aBcDeFgH",
+                    "field_types": {
+                      "network": {
+                        "regexp": "([a-z0-9]+\\.)*[a-z0-9]+",
+                        "placeholder": "irc.example.org"
+                      },
+                      "nickname": {
+                        "regexp": "[^\\s]+",
+                        "placeholder": "username"
+                      },
+                      "channel": {
+                        "regexp": "#[^\\s]+",
+                        "placeholder": "#foobar"
+                      }
+                    },
+                    "instances": [
+                      {
+                        "network_id": "freenode",
+                        "desc": "Freenode",
+                        "icon": "mxc://example.org/JkLmNoPq",
+                        "instance_id": "irc-freenode",
+                        "fields": {
+                          "network": "freenode.net"
+                        }
+                      }
+                    ]
+                  },
+                  "gitter": {
+                    "user_fields": ["username"],
+                    "location_fields": ["room"],
+                    "field_types": {
+                      "username": {
+                        "regexp": "@[^\\s]+",
+                        "placeholder": "@username"
+                      },
+                      "room": {
+                        "regexp": "[^\\s]+\\/[^\\s]+",
+                        "placeholder": "matrix-org/matrix-doc"
+                      }
+                    },
+                    "instances": [
+                      {
+                        "network_id": "gitter",
+                        "desc": "Gitter",
+                        "icon": "mxc://example.org/zXyWvUt",
+                        "instance_id": "gitter-gitter",
+                        "fields": {}
+                      }
+                    ]
+                  }
+                }
       tags:
         - Third-party Lookup
   "/thirdparty/protocol/{protocol}":
@@ -59,7 +117,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: ../application-service/definitions/protocol.yaml
+                $ref: definitions/protocol.yaml
         "404":
           description: The protocol is unknown.
           content:
diff --git a/data/api/server-server/public_rooms.yaml b/data/api/server-server/public_rooms.yaml
index 5bfa0f71f..565f1aa45 100644
--- a/data/api/server-server/public_rooms.yaml
+++ b/data/api/server-server/public_rooms.yaml
@@ -54,7 +54,10 @@ paths:
           description: |-
             The specific third-party network/protocol to request from the homeserver.
             Can only be used if `include_all_networks` is false.
-          example: irc
+
+            This is the `instance_id` of a `Protocol Instance` returned by
+            [`GET /_matrix/client/v3/thirdparty/protocols`](/client-server-api/#get_matrixclientv3thirdpartyprotocols).
+          example: irc-freenode
           schema:
             type: string
       responses:
@@ -124,7 +127,10 @@ paths:
                   description: |-
                     The specific third-party network/protocol to request from the
                     homeserver. Can only be used if `include_all_networks` is false.
-                  example: irc
+
+                    This is the `instance_id` of a `Protocol Instance` returned by
+                    [`GET /_matrix/client/v3/thirdparty/protocols`](/client-server-api/#get_matrixclientv3thirdpartyprotocols).
+                  example: irc-freenode
               example: {
                 "limit": 10,
                 "filter": {
@@ -135,7 +141,7 @@ paths:
                   ]
                 },
                 "include_all_networks": false,
-                "third_party_instance_id": "irc"
+                "third_party_instance_id": "irc-freenode"
               }
         description: Options for which rooms to return, or empty object to use defaults.
         required: true