diff --git a/lib/eslint/eslint-helpers.js b/lib/eslint/eslint-helpers.js
index 442686e56bf..8001ddd32ee 100644
--- a/lib/eslint/eslint-helpers.js
+++ b/lib/eslint/eslint-helpers.js
@@ -15,6 +15,7 @@ const fsp = fs.promises;
 const isGlob = require("is-glob");
 const globby = require("globby");
 const hash = require("../cli-engine/hash");
+const minimatch = require("minimatch");
 
 //-----------------------------------------------------------------------------
 // Errors
@@ -126,7 +127,7 @@ async function findFiles({
     const filePaths = patterns.map(filePath => path.resolve(cwd, filePath));
     const stats = await Promise.all(
         filePaths.map(
-            filePath => fsp.stat(filePath).catch(() => {})
+            filePath => fsp.stat(filePath).catch(() => { })
         )
     );
 
@@ -157,6 +158,11 @@ async function findFiles({
                             return false;
                         }
 
+                        // patterns starting with ** always apply
+                        if (filePattern.startsWith("**")) {
+                            return true;
+                        }
+
                         // patterns ending with * are not used for file search
                         if (filePattern.endsWith("*")) {
                             return false;
@@ -167,11 +173,27 @@ async function findFiles({
                             return false;
                         }
 
-                        // check if the pattern would be inside the cwd or not
+                        // check if the pattern would be inside the config base path or not
                         const fullFilePattern = path.join(cwd, filePattern);
-                        const relativeFilePattern = path.relative(configs.basePath, fullFilePattern);
+                        const patternRelativeToConfigBasePath = path.relative(configs.basePath, fullFilePattern);
+
+                        if (patternRelativeToConfigBasePath.startsWith("..")) {
+                            return false;
+                        }
+
+                        // check if the pattern matches
+                        if (minimatch(filePath, path.dirname(fullFilePattern), { partial: true })) {
+                            return true;
+                        }
+
+                        // check if the pattern is inside the directory or not
+                        const patternRelativeToFilePath = path.relative(filePath, fullFilePattern);
+
+                        if (patternRelativeToFilePath.startsWith("..")) {
+                            return false;
+                        }
 
-                        return !relativeFilePattern.startsWith("..");
+                        return true;
                     })
                     .map(filePattern => {
                         if (filePattern.startsWith("**")) {
diff --git a/tests/fixtures/shallow-glob/eslint.config.js b/tests/fixtures/shallow-glob/eslint.config.js
new file mode 100644
index 00000000000..211719ddb90
--- /dev/null
+++ b/tests/fixtures/shallow-glob/eslint.config.js
@@ -0,0 +1,5 @@
+module.exports = [
+    {
+        files: ["subdir/*.js"]
+    }
+];
diff --git a/tests/fixtures/shallow-glob/subdir/broken.js b/tests/fixtures/shallow-glob/subdir/broken.js
new file mode 100644
index 00000000000..d280fee2fdc
--- /dev/null
+++ b/tests/fixtures/shallow-glob/subdir/broken.js
@@ -0,0 +1 @@
+module.exports = /* intentional syntax error */
diff --git a/tests/fixtures/shallow-glob/subdir/subsubdir/broken.js b/tests/fixtures/shallow-glob/subdir/subsubdir/broken.js
new file mode 100644
index 00000000000..2e1fe2e76a2
--- /dev/null
+++ b/tests/fixtures/shallow-glob/subdir/subsubdir/broken.js
@@ -0,0 +1 @@
+function( {}   // intentional syntax error
diff --git a/tests/fixtures/shallow-glob/subdir/subsubdir/plain.jsx b/tests/fixtures/shallow-glob/subdir/subsubdir/plain.jsx
new file mode 100644
index 00000000000..e901f01b487
--- /dev/null
+++ b/tests/fixtures/shallow-glob/subdir/subsubdir/plain.jsx
@@ -0,0 +1 @@
+foo;
diff --git a/tests/fixtures/shallow-glob/target-dir/passing.js b/tests/fixtures/shallow-glob/target-dir/passing.js
new file mode 100644
index 00000000000..ec01c2c1416
--- /dev/null
+++ b/tests/fixtures/shallow-glob/target-dir/passing.js
@@ -0,0 +1 @@
+module.exports = true;
diff --git a/tests/lib/eslint/flat-eslint.js b/tests/lib/eslint/flat-eslint.js
index 1af6c2e1d8b..47d8cbbfbd8 100644
--- a/tests/lib/eslint/flat-eslint.js
+++ b/tests/lib/eslint/flat-eslint.js
@@ -784,6 +784,72 @@ describe("FlatESLint", () => {
             assert.strictEqual(results[0].suppressedMessages.length, 0);
         });
 
+        // https://github.com/eslint/eslint/issues/16260
+        describe("Globbing based on configs", () => {
+            it("should report zero messages when given a directory with a .js and config file specifying a subdirectory", async () => {
+                eslint = new FlatESLint({
+                    ignore: false,
+                    cwd: getFixturePath("shallow-glob")
+                });
+                const results = await eslint.lintFiles(["target-dir"]);
+
+                assert.strictEqual(results.length, 1);
+                assert.strictEqual(results[0].messages.length, 0);
+                assert.strictEqual(results[0].suppressedMessages.length, 0);
+            });
+
+            it("should glob for .jsx file in a subdirectory of the passed-in directory and not glob for any other patterns", async () => {
+                eslint = new FlatESLint({
+                    ignore: false,
+                    overrideConfigFile: true,
+                    overrideConfig: {
+                        files: ["subdir/**/*.jsx", "target-dir/*.js"],
+                        languageOptions: {
+                            parserOptions: {
+                                jsx: true
+                            }
+                        }
+                    },
+                    cwd: getFixturePath("shallow-glob")
+                });
+                const results = await eslint.lintFiles(["subdir/subsubdir"]);
+
+                assert.strictEqual(results.length, 2);
+                assert.strictEqual(results[0].messages.length, 1);
+                assert(results[0].messages[0].fatal, "Fatal error expected.");
+                assert.strictEqual(results[0].suppressedMessages.length, 0);
+                assert.strictEqual(results[1].messages.length, 0);
+                assert.strictEqual(results[1].suppressedMessages.length, 0);
+            });
+
+            it("should glob for all files in subdir when passed-in on the command line with a partial matching glob", async () => {
+                eslint = new FlatESLint({
+                    ignore: false,
+                    overrideConfigFile: true,
+                    overrideConfig: {
+                        files: ["s*/subsubdir/*.jsx", "target-dir/*.js"],
+                        languageOptions: {
+                            parserOptions: {
+                                jsx: true
+                            }
+                        }
+                    },
+                    cwd: getFixturePath("shallow-glob")
+                });
+                const results = await eslint.lintFiles(["subdir"]);
+
+                assert.strictEqual(results.length, 3);
+                assert.strictEqual(results[0].messages.length, 1);
+                assert(results[0].messages[0].fatal, "Fatal error expected.");
+                assert.strictEqual(results[0].suppressedMessages.length, 0);
+                assert.strictEqual(results[1].messages.length, 1);
+                assert(results[0].messages[0].fatal, "Fatal error expected.");
+                assert.strictEqual(results[1].suppressedMessages.length, 0);
+                assert.strictEqual(results[2].messages.length, 0);
+                assert.strictEqual(results[2].suppressedMessages.length, 0);
+            });
+        });
+
         it("should report zero messages when given a '**' pattern with a .js and a .js2 file", async () => {
             eslint = new FlatESLint({
                 ignore: false,