diff --git a/cli/config_file.rs b/cli/config_file.rs
index 7ccd861626..70576afc01 100644
--- a/cli/config_file.rs
+++ b/cli/config_file.rs
@@ -885,14 +885,14 @@ mod tests {
   fn discover_inner_success() {
     // testdata/fmt/deno.jsonc exists
     let testdata = test_util::testdata_path();
-    let c_md = testdata.join("fmt/fmt_with_config/c.md");
+    let c_md = testdata.join("fmt/with_config/subdir/c.md");
     let mut checked = HashSet::new();
     let config_file = discover_inner(&c_md, &mut checked).unwrap().unwrap();
     assert!(checked.contains(c_md.parent().unwrap()));
     assert!(!checked.contains(&testdata));
     let fmt_config = config_file.to_fmt_config().unwrap().unwrap();
     let expected_exclude = ModuleSpecifier::from_file_path(
-      testdata.join("fmt/fmt_with_config/b.ts"),
+      testdata.join("fmt/with_config/subdir/b.ts"),
     )
     .unwrap();
     assert_eq!(fmt_config.files.exclude, vec![expected_exclude]);
diff --git a/cli/fs_util.rs b/cli/fs_util.rs
index 20b20cccdb..339f6764f4 100644
--- a/cli/fs_util.rs
+++ b/cli/fs_util.rs
@@ -136,31 +136,6 @@ pub fn is_supported_ext(path: &Path) -> bool {
   }
 }
 
-/// This function is similar to is_supported_ext but adds additional extensions
-/// supported by `deno fmt`.
-pub fn is_supported_ext_fmt(path: &Path) -> bool {
-  if let Some(ext) = get_extension(path) {
-    matches!(
-      ext.as_str(),
-      "ts"
-        | "tsx"
-        | "js"
-        | "jsx"
-        | "mjs"
-        | "json"
-        | "jsonc"
-        | "md"
-        | "mkd"
-        | "mkdn"
-        | "mdwn"
-        | "mdown"
-        | "markdown"
-    )
-  } else {
-    false
-  }
-}
-
 /// Checks if the path has a basename and extension Deno supports for tests.
 pub fn is_supported_test_path(path: &Path) -> bool {
   use std::path::Component;
@@ -446,43 +421,11 @@ mod tests {
     assert!(!is_supported_ext(Path::new("foo.mjsx")));
   }
 
-  #[test]
-  fn test_is_supported_ext_fmt() {
-    assert!(!is_supported_ext_fmt(Path::new("tests/subdir/redirects")));
-    assert!(is_supported_ext_fmt(Path::new("README.md")));
-    assert!(is_supported_ext_fmt(Path::new("readme.MD")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mkd")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mkdn")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mdwn")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mdown")));
-    assert!(is_supported_ext_fmt(Path::new("readme.markdown")));
-    assert!(is_supported_ext_fmt(Path::new("lib/typescript.d.ts")));
-    assert!(is_supported_ext_fmt(Path::new("testdata/001_hello.js")));
-    assert!(is_supported_ext_fmt(Path::new("testdata/002_hello.ts")));
-    assert!(is_supported_ext_fmt(Path::new("foo.jsx")));
-    assert!(is_supported_ext_fmt(Path::new("foo.tsx")));
-    assert!(is_supported_ext_fmt(Path::new("foo.TS")));
-    assert!(is_supported_ext_fmt(Path::new("foo.TSX")));
-    assert!(is_supported_ext_fmt(Path::new("foo.JS")));
-    assert!(is_supported_ext_fmt(Path::new("foo.JSX")));
-    assert!(is_supported_ext_fmt(Path::new("foo.mjs")));
-    assert!(!is_supported_ext_fmt(Path::new("foo.mjsx")));
-    assert!(is_supported_ext_fmt(Path::new("foo.jsonc")));
-    assert!(is_supported_ext_fmt(Path::new("foo.JSONC")));
-    assert!(is_supported_ext_fmt(Path::new("foo.json")));
-    assert!(is_supported_ext_fmt(Path::new("foo.JsON")));
-  }
-
   #[test]
   fn test_is_supported_test_ext() {
     assert!(!is_supported_test_ext(Path::new("tests/subdir/redirects")));
     assert!(is_supported_test_ext(Path::new("README.md")));
     assert!(is_supported_test_ext(Path::new("readme.MD")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mkd")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mkdn")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mdwn")));
-    assert!(is_supported_ext_fmt(Path::new("readme.mdown")));
-    assert!(is_supported_ext_fmt(Path::new("readme.markdown")));
     assert!(is_supported_test_ext(Path::new("lib/typescript.d.ts")));
     assert!(is_supported_test_ext(Path::new("testdata/001_hello.js")));
     assert!(is_supported_test_ext(Path::new("testdata/002_hello.ts")));
diff --git a/cli/tests/integration/fmt_tests.rs b/cli/tests/integration/fmt_tests.rs
index f1847d3a72..df2fe182e7 100644
--- a/cli/tests/integration/fmt_tests.rs
+++ b/cli/tests/integration/fmt_tests.rs
@@ -177,18 +177,18 @@ itest!(fmt_stdin_check_not_formatted {
 });
 
 itest!(fmt_with_config {
-  args: "fmt --config fmt/deno.jsonc fmt/fmt_with_config/",
+  args: "fmt --config fmt/with_config/deno.jsonc fmt/with_config/subdir",
   output: "fmt/fmt_with_config.out",
 });
 
 itest!(fmt_with_config_default {
-  args: "fmt fmt/fmt_with_config/",
+  args: "fmt fmt/with_config/subdir",
   output: "fmt/fmt_with_config.out",
 });
 
 // Check if CLI flags take precedence
 itest!(fmt_with_config_and_flags {
-  args: "fmt --config fmt/deno.jsonc --ignore=fmt/fmt_with_config/a.ts,fmt/fmt_with_config/b.ts",
+  args: "fmt --config fmt/with_config/deno.jsonc --ignore=fmt/with_config/subdir/a.ts,fmt/with_config/subdir/b.ts",
   output: "fmt/fmt_with_config_and_flags.out",
 });
 
diff --git a/cli/tests/testdata/fmt/deno.jsonc b/cli/tests/testdata/fmt/deno.jsonc
deleted file mode 100644
index 9c330d34a8..0000000000
--- a/cli/tests/testdata/fmt/deno.jsonc
+++ /dev/null
@@ -1,15 +0,0 @@
-{
-  "fmt": {
-    "files": {
-      "include": ["fmt_with_config/"],
-      "exclude": ["fmt_with_config/b.ts"]
-    },
-    "options": {
-      "useTabs": true,
-      "lineWidth": 40,
-      "indentWidth": 8,
-      "singleQuote": true,
-      "proseWrap": "always"
-    }
-  }
-}
diff --git a/cli/tests/testdata/fmt/with_config/deno.jsonc b/cli/tests/testdata/fmt/with_config/deno.jsonc
new file mode 100644
index 0000000000..3b9474e644
--- /dev/null
+++ b/cli/tests/testdata/fmt/with_config/deno.jsonc
@@ -0,0 +1,19 @@
+{
+	"fmt": {
+		"files": {
+			"include": [
+				"./subdir/"
+			],
+			"exclude": [
+				"./subdir/b.ts"
+			]
+		},
+		"options": {
+			"useTabs": true,
+			"lineWidth": 40,
+			"indentWidth": 8,
+			"singleQuote": true,
+			"proseWrap": "always"
+		}
+	}
+}
diff --git a/cli/tests/testdata/fmt/fmt_with_config/a.ts b/cli/tests/testdata/fmt/with_config/subdir/a.ts
similarity index 100%
rename from cli/tests/testdata/fmt/fmt_with_config/a.ts
rename to cli/tests/testdata/fmt/with_config/subdir/a.ts
diff --git a/cli/tests/testdata/fmt/fmt_with_config/b.ts b/cli/tests/testdata/fmt/with_config/subdir/b.ts
similarity index 100%
rename from cli/tests/testdata/fmt/fmt_with_config/b.ts
rename to cli/tests/testdata/fmt/with_config/subdir/b.ts
diff --git a/cli/tests/testdata/fmt/fmt_with_config/c.md b/cli/tests/testdata/fmt/with_config/subdir/c.md
similarity index 100%
rename from cli/tests/testdata/fmt/fmt_with_config/c.md
rename to cli/tests/testdata/fmt/with_config/subdir/c.md
diff --git a/cli/tools/fmt.rs b/cli/tools/fmt.rs
index 9172421b51..ebcdc6dd23 100644
--- a/cli/tools/fmt.rs
+++ b/cli/tools/fmt.rs
@@ -16,7 +16,7 @@ use crate::file_watcher;
 use crate::file_watcher::ResolutionResult;
 use crate::flags::FmtFlags;
 use crate::fs_util::specifier_to_file_path;
-use crate::fs_util::{collect_files, get_extension, is_supported_ext_fmt};
+use crate::fs_util::{collect_files, get_extension};
 use crate::text_encoding;
 use deno_ast::ParsedSource;
 use deno_core::anyhow::Context;
@@ -91,6 +91,7 @@ pub async fn format(
     let result =
       collect_files(&include_files, &exclude_files, is_supported_ext_fmt).map(
         |files| {
+          eprintln!("fmt files {:?}", files);
           let refmt_files = if let Some(paths) = changed {
             if check {
               files
@@ -597,3 +598,55 @@ where
     Ok(())
   }
 }
+
+/// This function is similar to is_supported_ext but adds additional extensions
+/// supported by `deno fmt`.
+fn is_supported_ext_fmt(path: &Path) -> bool {
+  if let Some(ext) = get_extension(path) {
+    matches!(
+      ext.as_str(),
+      "ts"
+        | "tsx"
+        | "js"
+        | "jsx"
+        | "mjs"
+        | "json"
+        | "jsonc"
+        | "md"
+        | "mkd"
+        | "mkdn"
+        | "mdwn"
+        | "mdown"
+        | "markdown"
+    )
+  } else {
+    false
+  }
+}
+
+#[test]
+fn test_is_supported_ext_fmt() {
+  assert!(!is_supported_ext_fmt(Path::new("tests/subdir/redirects")));
+  assert!(is_supported_ext_fmt(Path::new("README.md")));
+  assert!(is_supported_ext_fmt(Path::new("readme.MD")));
+  assert!(is_supported_ext_fmt(Path::new("readme.mkd")));
+  assert!(is_supported_ext_fmt(Path::new("readme.mkdn")));
+  assert!(is_supported_ext_fmt(Path::new("readme.mdwn")));
+  assert!(is_supported_ext_fmt(Path::new("readme.mdown")));
+  assert!(is_supported_ext_fmt(Path::new("readme.markdown")));
+  assert!(is_supported_ext_fmt(Path::new("lib/typescript.d.ts")));
+  assert!(is_supported_ext_fmt(Path::new("testdata/001_hello.js")));
+  assert!(is_supported_ext_fmt(Path::new("testdata/002_hello.ts")));
+  assert!(is_supported_ext_fmt(Path::new("foo.jsx")));
+  assert!(is_supported_ext_fmt(Path::new("foo.tsx")));
+  assert!(is_supported_ext_fmt(Path::new("foo.TS")));
+  assert!(is_supported_ext_fmt(Path::new("foo.TSX")));
+  assert!(is_supported_ext_fmt(Path::new("foo.JS")));
+  assert!(is_supported_ext_fmt(Path::new("foo.JSX")));
+  assert!(is_supported_ext_fmt(Path::new("foo.mjs")));
+  assert!(!is_supported_ext_fmt(Path::new("foo.mjsx")));
+  assert!(is_supported_ext_fmt(Path::new("foo.jsonc")));
+  assert!(is_supported_ext_fmt(Path::new("foo.JSONC")));
+  assert!(is_supported_ext_fmt(Path::new("foo.json")));
+  assert!(is_supported_ext_fmt(Path::new("foo.JsON")));
+}