diff --git a/cmd/cli.go b/cmd/cli.go
index 4a72471f4..6904d23e7 100644
--- a/cmd/cli.go
+++ b/cmd/cli.go
@@ -14,6 +14,7 @@ import (
 	"github.com/fatih/color"
 	"github.com/hashicorp/logutils"
 	flags "github.com/jessevdk/go-flags"
+	"github.com/spf13/afero"
 	"github.com/terraform-linters/tflint/formatter"
 	"github.com/terraform-linters/tflint/terraform"
 	"github.com/terraform-linters/tflint/tflint"
@@ -54,19 +55,46 @@ func NewCLI(outStream io.Writer, errStream io.Writer) (*CLI, error) {
 
 // Run invokes the CLI with the given arguments.
 func (cli *CLI) Run(args []string) int {
+	cli.formatter = &formatter.Formatter{
+		Stdout: cli.outStream,
+		Stderr: cli.errStream,
+	}
+
+	// Configure options parser
 	var opts Options
 	parser := flags.NewParser(&opts, flags.HelpFlag)
 	parser.Usage = "--chdir=DIR/--recursive [OPTIONS]"
 	parser.UnknownOptionHandler = unknownOptionHandler
-	// Parse commandline flag
+
+	// Parse command line options
 	args, err := parser.ParseArgs(args)
-	// Set up output formatter
-	cli.formatter = &formatter.Formatter{
-		Stdout: cli.outStream,
-		Stderr: cli.errStream,
-		Format: opts.Format,
-		Fix:    opts.Fix,
+	if err != nil {
+		if flagsErr, ok := err.(*flags.Error); ok && flagsErr.Type == flags.ErrHelp {
+			fmt.Fprintln(cli.outStream, err)
+			return ExitCodeOK
+		}
+		cli.formatter.Print(tflint.Issues{}, fmt.Errorf("Failed to parse CLI options; %w", err), map[string][]byte{})
+		return ExitCodeError
+	}
+
+	if len(args) > 1 {
+		cli.formatter.Print(tflint.Issues{}, fmt.Errorf("Command line arguments support was dropped in v0.47. Use --chdir or --filter instead."), map[string][]byte{})
+		return ExitCodeError
+	}
+
+	// Setup config
+	cfg, err := tflint.LoadConfig(afero.Afero{Fs: afero.NewOsFs()}, opts.Config)
+	if err != nil {
+		fmt.Fprintf(cli.errStream, "Failed to load TFLint config; %s\n", err)
+		return ExitCodeError
 	}
+
+	cfg.Merge(opts.toConfig())
+
+	// Set formatter fields from options/config
+	cli.formatter.Format = cfg.Format
+	cli.formatter.Fix = opts.Fix
+
 	if opts.Color {
 		color.NoColor = false
 		cli.formatter.NoColor = false
@@ -83,18 +111,6 @@ func (cli *CLI) Run(args []string) int {
 	})
 	log.SetFlags(log.Ltime | log.Lshortfile)
 
-	if err != nil {
-		if flagsErr, ok := err.(*flags.Error); ok && flagsErr.Type == flags.ErrHelp {
-			fmt.Fprintln(cli.outStream, err)
-			return ExitCodeOK
-		}
-		cli.formatter.Print(tflint.Issues{}, fmt.Errorf("Failed to parse CLI options; %w", err), map[string][]byte{})
-		return ExitCodeError
-	}
-	if len(args) > 1 {
-		cli.formatter.Print(tflint.Issues{}, fmt.Errorf("Command line arguments support was dropped in v0.47. Use --chdir or --filter instead."), map[string][]byte{})
-		return ExitCodeError
-	}
 	if opts.MaxWorkers != nil && *opts.MaxWorkers <= 0 {
 		cli.formatter.Print(tflint.Issues{}, fmt.Errorf("Max workers should be greater than 0"), map[string][]byte{})
 		return ExitCodeError
diff --git a/integrationtest/cli/cli_test.go b/integrationtest/cli/cli_test.go
index 55224169a..5061807a6 100644
--- a/integrationtest/cli/cli_test.go
+++ b/integrationtest/cli/cli_test.go
@@ -50,11 +50,25 @@ func TestIntegration(t *testing.T) {
 			stdout:  "",
 		},
 		{
-			name:    "specify format",
+			name:    "format flag",
 			command: "./tflint --format json",
 			dir:     "no_issues",
 			status:  cmd.ExitCodeOK,
-			stdout:  "[]",
+			stdout:  `{"issues":[],"errors":[]}`,
+		},
+		{
+			name:    "format config",
+			command: "./tflint",
+			dir:     "format_config",
+			status:  cmd.ExitCodeIssuesFound,
+			stdout:  `main.tf:2:19: Error - instance type is t2.micro (aws_instance_example_type)`,
+		},
+		{
+			name:    "format flag overrides config",
+			command: "./tflint --format json",
+			dir:     "format_config",
+			status:  cmd.ExitCodeIssuesFound,
+			stdout:  `{"issues":[{"rule":{"name":"aws_instance_example_type","severity":"error","link":""},"message":"instance type is t2.micro","range":{"filename":"main.tf","start":{"line":2,"column":19},"end":{"line":2,"column":29}},"callers":[]}],"errors":[]}`,
 		},
 		{
 			name:    "`--force` option with no issues",
diff --git a/integrationtest/cli/format_config/.tflint.hcl b/integrationtest/cli/format_config/.tflint.hcl
new file mode 100644
index 000000000..d60d16448
--- /dev/null
+++ b/integrationtest/cli/format_config/.tflint.hcl
@@ -0,0 +1,7 @@
+config {
+  format = "compact"
+}
+
+plugin "testing" {
+  enabled = true
+}
diff --git a/integrationtest/cli/format_config/main.tf b/integrationtest/cli/format_config/main.tf
new file mode 100644
index 000000000..b73b98751
--- /dev/null
+++ b/integrationtest/cli/format_config/main.tf
@@ -0,0 +1,3 @@
+resource "aws_instance" "main" {
+  instance_type = "t2.micro"
+}
diff --git a/integrationtest/recursive/recursive_test.go b/integrationtest/recursive/recursive_test.go
index f83e634ef..aaa50ea9a 100644
--- a/integrationtest/recursive/recursive_test.go
+++ b/integrationtest/recursive/recursive_test.go
@@ -92,6 +92,14 @@ func TestIntegration(t *testing.T) {
 
 			opts := []cmp.Option{
 				cmpopts.IgnoreFields(formatter.JSONRule{}, "Link"),
+				// Only compare error messages up to the double new line.
+				// After this, stderr will be printed which is verbose.
+				cmp.Transformer("TruncateMessage", func(e formatter.JSONError) formatter.JSONError {
+					if parts := strings.Split(e.Message, "\n\n"); len(parts) > 1 {
+						e.Message = parts[0]
+					}
+					return e
+				}),
 			}
 			if test.ignoreOrder {
 				opts = append(opts, cmpopts.SortSlices(func(a, b formatter.JSONError) bool {