diff --git a/packages/integrations/mdx/src/index.ts b/packages/integrations/mdx/src/index.ts
index 6fb96de9a..3e9cc945c 100644
--- a/packages/integrations/mdx/src/index.ts
+++ b/packages/integrations/mdx/src/index.ts
@@ -11,7 +11,7 @@ import type { Options as RemarkRehypeOptions } from 'remark-rehype';
 import { VFile } from 'vfile';
 import type { Plugin as VitePlugin } from 'vite';
 import { getRehypePlugins, getRemarkPlugins, recmaInjectImportMetaEnvPlugin } from './plugins.js';
-import { getFileInfo, parseFrontmatter } from './utils.js';
+import { getFileInfo, parseFrontmatter, ignoreStringPlugins } from './utils.js';
 
 export type MdxOptions = Omit<typeof markdownConfigDefaults, 'remarkPlugins' | 'rehypePlugins'> & {
 	extendMarkdownConfig: boolean;
@@ -70,7 +70,7 @@ export default function mdx(partialMdxOptions: Partial<MdxOptions> = {}): Integr
 
 				const mdxOptions = applyDefaultOptions({
 					options: partialMdxOptions,
-					defaults: withDefaultMdxOptions(extendMarkdownConfig ? config.markdown : markdownConfigDefaults),
+					defaults: markdownConfigToMdxOptions(extendMarkdownConfig ? config.markdown : markdownConfigDefaults),
 				});
 
 				const mdxPluginOpts: MdxRollupPluginOptions = {
@@ -188,15 +188,15 @@ export default function mdx(partialMdxOptions: Partial<MdxOptions> = {}): Integr
 const defaultMdxOptions = {
 	extendMarkdownConfig: true,
 	recmaPlugins: [],
-	remarkPlugins: [],
-	rehypePlugins: [],
-	remarkRehype: {},
 }
 
-function withDefaultMdxOptions(markdownConfig: typeof markdownConfigDefaults): MdxOptions {
+function markdownConfigToMdxOptions(markdownConfig: typeof markdownConfigDefaults): MdxOptions {
 	return {
-		...markdownConfig,
 		...defaultMdxOptions,
+		...markdownConfig,
+		remarkPlugins: ignoreStringPlugins(markdownConfig.remarkPlugins),
+		rehypePlugins: ignoreStringPlugins(markdownConfig.rehypePlugins),
+		remarkRehype: markdownConfig.remarkRehype as any ?? {},
 	};
 }
 
diff --git a/packages/integrations/mdx/src/plugins.ts b/packages/integrations/mdx/src/plugins.ts
index cff09eae8..b0651a53b 100644
--- a/packages/integrations/mdx/src/plugins.ts
+++ b/packages/integrations/mdx/src/plugins.ts
@@ -4,12 +4,11 @@ import {
 	safelyGetAstroData,
 } from '@astrojs/markdown-remark/dist/internal.js';
 import { nodeTypes } from '@mdx-js/mdx';
-import type { PluggableList } from '@mdx-js/mdx/lib/core.js';
 import type { Options as MdxRollupPluginOptions } from '@mdx-js/rollup';
+import type { PluggableList } from '@mdx-js/mdx/lib/core.js';
 import type { AstroConfig } from 'astro';
 import type { Literal, MemberExpression } from 'estree';
 import { visit as estreeVisit } from 'estree-util-visit';
-import { bold, yellow } from 'kleur/colors';
 import type { Image } from 'mdast';
 import { pathToFileURL } from 'node:url';
 import rehypeRaw from 'rehype-raw';
@@ -142,7 +141,7 @@ export async function getRemarkPlugins(
 		}
 	}
 
-	remarkPlugins = [...remarkPlugins, ...ignoreStringPlugins(mdxOptions.remarkPlugins)];
+	remarkPlugins = [...remarkPlugins, ...mdxOptions.remarkPlugins];
 
 	if (!isPerformanceBenchmark) {
 		// Apply syntax highlighters after user plugins to match `markdown/remark` behavior
@@ -169,7 +168,7 @@ export function getRehypePlugins(mdxOptions: MdxOptions): MdxRollupPluginOptions
 
 	rehypePlugins = [
 		...rehypePlugins,
-		...ignoreStringPlugins(mdxOptions.rehypePlugins),
+		...mdxOptions.rehypePlugins,
 		// getHeadings() is guaranteed by TS, so this must be included.
 		// We run `rehypeHeadingIds` _last_ to respect any custom IDs set by user plugins.
 		...(isPerformanceBenchmark ? [] : [rehypeHeadingIds, rehypeInjectHeadingsExport]),
@@ -179,28 +178,6 @@ export function getRehypePlugins(mdxOptions: MdxOptions): MdxRollupPluginOptions
 	return rehypePlugins;
 }
 
-function ignoreStringPlugins(plugins: any[]): PluggableList {
-	let validPlugins: PluggableList = [];
-	let hasInvalidPlugin = false;
-	for (const plugin of plugins) {
-		if (typeof plugin === 'string') {
-			console.warn(yellow(`[MDX] ${bold(plugin)} not applied.`));
-			hasInvalidPlugin = true;
-		} else if (Array.isArray(plugin) && typeof plugin[0] === 'string') {
-			console.warn(yellow(`[MDX] ${bold(plugin[0])} not applied.`));
-			hasInvalidPlugin = true;
-		} else {
-			validPlugins.push(plugin);
-		}
-	}
-	if (hasInvalidPlugin) {
-		console.warn(
-			`To inherit Markdown plugins in MDX, please use explicit imports in your config instead of "strings." See Markdown docs: https://docs.astro.build/en/guides/markdown-content/#markdown-plugins`
-		);
-	}
-	return validPlugins;
-}
-
 /**
  * Check if estree entry is "import.meta.env.VARIABLE"
  * If it is, return the variable name (i.e. "VARIABLE")
diff --git a/packages/integrations/mdx/src/utils.ts b/packages/integrations/mdx/src/utils.ts
index 516cfafb2..1f679f9fa 100644
--- a/packages/integrations/mdx/src/utils.ts
+++ b/packages/integrations/mdx/src/utils.ts
@@ -1,7 +1,9 @@
 import type { Options as AcornOpts } from 'acorn';
 import { parse } from 'acorn';
 import type { AstroConfig, SSRError } from 'astro';
+import { bold, yellow } from 'kleur/colors';
 import matter from 'gray-matter';
+import type { PluggableList } from '@mdx-js/mdx/lib/core.js';
 import type { MdxjsEsm } from 'mdast-util-mdx';
 
 function appendForwardSlash(path: string) {
@@ -100,3 +102,25 @@ function startsWithDotSlash(path: string) {
 	const c2 = path[1];
 	return c1 === '.' && c2 === '/';
 }
+
+export function ignoreStringPlugins(plugins: any[]): PluggableList {
+	let validPlugins: PluggableList = [];
+	let hasInvalidPlugin = false;
+	for (const plugin of plugins) {
+		if (typeof plugin === 'string') {
+			console.warn(yellow(`[MDX] ${bold(plugin)} not applied.`));
+			hasInvalidPlugin = true;
+		} else if (Array.isArray(plugin) && typeof plugin[0] === 'string') {
+			console.warn(yellow(`[MDX] ${bold(plugin[0])} not applied.`));
+			hasInvalidPlugin = true;
+		} else {
+			validPlugins.push(plugin);
+		}
+	}
+	if (hasInvalidPlugin) {
+		console.warn(
+			`To inherit Markdown plugins in MDX, please use explicit imports in your config instead of "strings." See Markdown docs: https://docs.astro.build/en/guides/markdown-content/#markdown-plugins`
+		);
+	}
+	return validPlugins;
+}