diff --git a/.changeset/short-suits-knock.md b/.changeset/short-suits-knock.md
new file mode 100644
index 0000000000..b6b84a7f22
--- /dev/null
+++ b/.changeset/short-suits-knock.md
@@ -0,0 +1,5 @@
+---
+"stylelint": patch
+---
+
+Fixed: `custom-property-empty-line-before` false positives for CSS-in-JS
diff --git a/lib/__tests__/fixtures/postcss-naive-css-in-js.js b/lib/__tests__/fixtures/postcss-naive-css-in-js.js
new file mode 100644
index 0000000000..4ebf18c14b
--- /dev/null
+++ b/lib/__tests__/fixtures/postcss-naive-css-in-js.js
@@ -0,0 +1,34 @@
+const postcss = require('postcss');
+
+/**
+ * @type {postcss.Parser<postcss.Document>}
+ */
+function parse(css) {
+	const source = typeof css === 'string' ? css : css.toString();
+
+	const document = postcss.document({
+		source: {
+			input: new postcss.Input(source),
+		},
+	});
+
+	// E.g. "css` color: red; `;"
+	for (const match of source.matchAll(/\bcss`([^`]+)`;/g)) {
+		document.append(postcss.parse(match[1]));
+	}
+
+	return document;
+}
+
+/**
+ * @type {postcss.Stringifier}
+ */
+function stringify(node, builder) {
+	if (node.type === 'document') {
+		node.each((root) => {
+			builder(`css\`${root}\`;`, root);
+		});
+	}
+}
+
+module.exports = { parse, stringify };
diff --git a/lib/rules/custom-property-empty-line-before/__tests__/index.js b/lib/rules/custom-property-empty-line-before/__tests__/index.js
index f48906acd9..91de21b81a 100644
--- a/lib/rules/custom-property-empty-line-before/__tests__/index.js
+++ b/lib/rules/custom-property-empty-line-before/__tests__/index.js
@@ -1,5 +1,7 @@
 'use strict';
 
+const naiveCssInJs = require('../../../__tests__/fixtures/postcss-naive-css-in-js');
+
 const { messages, ruleName } = require('..');
 
 testRule({
@@ -570,3 +572,15 @@ testRule({
 		},
 	],
 });
+
+testRule({
+	ruleName,
+	config: ['always', { except: ['first-nested'] }],
+	customSyntax: naiveCssInJs,
+
+	accept: [
+		{
+			code: 'css` --foo: 100px; `;',
+		},
+	],
+});
diff --git a/lib/utils/__tests__/isFirstNested.test.js b/lib/utils/__tests__/isFirstNested.test.js
index 6e699bc0a4..8c09bb64bb 100644
--- a/lib/utils/__tests__/isFirstNested.test.js
+++ b/lib/utils/__tests__/isFirstNested.test.js
@@ -161,4 +161,26 @@ describe('isFirstNested', () => {
 		expect(isFirstNested(decls[2])).toBe(false);
 		expect(isFirstNested(decls[3])).toBe(false);
 	});
+
+	it('returns false without a parent', () => {
+		const decl = postcss.decl({ prop: 'color', value: 'pink' });
+
+		expect(isFirstNested(decl)).toBe(false);
+	});
+
+	it('returns true with the first-nested declaration in a document', () => {
+		const document = postcss.document();
+
+		document.append(postcss.parse('color: pink;'));
+		document.append(postcss.parse('color: red; color: blue;'));
+
+		const decls = [];
+
+		document.walkDecls('color', (decl) => decls.push(decl));
+
+		expect(decls).toHaveLength(3);
+		expect(isFirstNested(decls[0])).toBe(true);
+		expect(isFirstNested(decls[1])).toBe(true);
+		expect(isFirstNested(decls[2])).toBe(false);
+	});
 });
diff --git a/lib/utils/isFirstNested.js b/lib/utils/isFirstNested.js
index 2aa3788e00..56c55275c3 100644
--- a/lib/utils/isFirstNested.js
+++ b/lib/utils/isFirstNested.js
@@ -1,6 +1,6 @@
 'use strict';
 
-const { isComment, hasSource } = require('./typeGuards');
+const { isComment, isDocument, isRoot, hasSource } = require('./typeGuards');
 
 /**
  * @param {import('postcss').Node} statement
@@ -9,7 +9,11 @@ const { isComment, hasSource } = require('./typeGuards');
 module.exports = function isFirstNested(statement) {
 	const parentNode = statement.parent;
 
-	if (parentNode === undefined || parentNode.type === 'root') {
+	if (parentNode === undefined) {
+		return false;
+	}
+
+	if (isRoot(parentNode) && !isInDocument(parentNode)) {
 		return false;
 	}
 
@@ -71,3 +75,11 @@ module.exports = function isFirstNested(statement) {
 	/* istanbul ignore next: Should always return in the loop */
 	return false;
 };
+
+/**
+ * @param {import('postcss').Node} node
+ * @returns {boolean}
+ */
+function isInDocument({ parent }) {
+	return Boolean(parent && isDocument(parent));
+}
diff --git a/lib/utils/typeGuards.js b/lib/utils/typeGuards.js
index 2bf6a4624e..705cccef70 100644
--- a/lib/utils/typeGuards.js
+++ b/lib/utils/typeGuards.js
@@ -1,7 +1,7 @@
 'use strict';
 
 /** @typedef {import('postcss').Node} Node */
-/** @typedef {import('postcss').Node} NodeSource */
+/** @typedef {import('postcss').Source} NodeSource */
 
 /**
  * @param {Node} node
@@ -43,6 +43,14 @@ module.exports.isDeclaration = function isDeclaration(node) {
 	return node.type === 'decl';
 };
 
+/**
+ * @param {Node} node
+ * @returns {node is import('postcss').Document}
+ */
+module.exports.isDocument = function isDocument(node) {
+	return node.type === 'document';
+};
+
 /**
  * @param {import('postcss-value-parser').Node} node
  * @returns {node is import('postcss-value-parser').FunctionNode}