diff --git a/.changeset/sour-tables-lick.md b/.changeset/sour-tables-lick.md
new file mode 100644
index 0000000000..3c2c5cf6cf
--- /dev/null
+++ b/.changeset/sour-tables-lick.md
@@ -0,0 +1,5 @@
+---
+"stylelint": patch
+---
+
+Fixed: `allowEmptyInput` in configuration files
diff --git a/lib/__tests__/fixtures/config-allow-empty-input.json b/lib/__tests__/fixtures/config-allow-empty-input.json
new file mode 100644
index 0000000000..69bd0d0436
--- /dev/null
+++ b/lib/__tests__/fixtures/config-allow-empty-input.json
@@ -0,0 +1,4 @@
+{
+	"allowEmptyInput": true,
+	"rules": {}
+}
diff --git a/lib/__tests__/standalone.test.js b/lib/__tests__/standalone.test.js
index 219d3876ee..bde31b0c3e 100644
--- a/lib/__tests__/standalone.test.js
+++ b/lib/__tests__/standalone.test.js
@@ -178,6 +178,17 @@ it('standalone with nonexistent-file and allowEmptyInput enabled (in config) qui
 	expect(output).toBe('[]');
 });
 
+it('standalone with nonexistent-file and allowEmptyInput enabled (in config file) quietly exits', async () => {
+	const { results, errored, output } = await standalone({
+		files: `${fixturesPath}/nonexistent-file.css`,
+		configFile: `${fixturesPath}/config-allow-empty-input.json`,
+	});
+
+	expect(results).toHaveLength(0);
+	expect(errored).toBe(false);
+	expect(output).toBe('[]');
+});
+
 describe('standalone passing code with syntax error', () => {
 	let results;
 
diff --git a/lib/standalone.js b/lib/standalone.js
index ceed4f4b24..a7ed9058a5 100644
--- a/lib/standalone.js
+++ b/lib/standalone.js
@@ -11,6 +11,7 @@ const createStylelint = require('./createStylelint');
 const createPartialStylelintResult = require('./createPartialStylelintResult');
 const filterFilePaths = require('./utils/filterFilePaths');
 const formatters = require('./formatters');
+const getConfigForFile = require('./getConfigForFile');
 const getFileIgnorer = require('./utils/getFileIgnorer');
 const getFormatterOptionsText = require('./utils/getFormatterOptionsText');
 const lintSource = require('./lintSource');
@@ -251,7 +252,7 @@ async function standalone({
 		});
 
 		stylelintResults = await Promise.all(getStylelintResults);
-	} else if (allowEmptyInput ?? config?.allowEmptyInput) {
+	} else if (allowEmptyInput ?? config?.allowEmptyInput ?? (await canAllowEmptyInput(stylelint))) {
 		stylelintResults = await Promise.all([]);
 	} else if (filePathsLengthBeforeIgnore) {
 		// All input files ignored
@@ -311,4 +312,14 @@ function handleError(error) {
 	throw error;
 }
 
+/**
+ * @param {import('stylelint').InternalApi} stylelint
+ * @returns {Promise<boolean>}
+ */
+async function canAllowEmptyInput(stylelint) {
+	const config = await getConfigForFile(stylelint);
+
+	return Boolean(config?.config?.allowEmptyInput);
+}
+
 module.exports = standalone;