diff --git a/.changeset/slimy-cobras-end.md b/.changeset/slimy-cobras-end.md
new file mode 100644
index 000000000000..e87571c2ee11
--- /dev/null
+++ b/.changeset/slimy-cobras-end.md
@@ -0,0 +1,7 @@
+---
+"@astrojs/mdx": major
+---
+
+Allows integrations after the MDX integration to update `markdown.remarkPlugins` and `markdown.rehypePlugins`, and have the plugins work in MDX too.
+
+If you rely on the ordering before to not add remark/rehype plugins for MDX, you need to configure `@astrojs/mdx` with `extendMarkdownConfig: false` and explicitly specify the `remarkPlugins` and `rehypePlugins` options instead.
diff --git a/packages/integrations/mdx/src/index.ts b/packages/integrations/mdx/src/index.ts
index cc831704ff9e..3aaed8787585 100644
--- a/packages/integrations/mdx/src/index.ts
+++ b/packages/integrations/mdx/src/index.ts
@@ -29,6 +29,10 @@ type SetupHookParams = HookParameters<'astro:config:setup'> & {
 };
 
 export default function mdx(partialMdxOptions: Partial<MdxOptions> = {}): AstroIntegration {
+	// @ts-expect-error Temporarily assign an empty object here, which will be re-assigned by the
+	// `astro:config:done` hook later. This is so that `vitePluginMdx` can get hold of a reference earlier.
+	let mdxOptions: MdxOptions = {};
+
 	return {
 		name: '@astrojs/mdx',
 		hooks: {
@@ -58,21 +62,30 @@ export default function mdx(partialMdxOptions: Partial<MdxOptions> = {}): AstroI
 					handlePropagation: true,
 				});
 
+				updateConfig({
+					vite: {
+						plugins: [vitePluginMdx(mdxOptions), vitePluginMdxPostprocess(config)],
+					},
+				});
+			},
+			'astro:config:done': ({ config }) => {
+				// We resolve the final MDX options here so that other integrations have a chance to modify
+				// `config.markdown` before we access it
 				const extendMarkdownConfig =
 					partialMdxOptions.extendMarkdownConfig ?? defaultMdxOptions.extendMarkdownConfig;
 
-				const mdxOptions = applyDefaultOptions({
+				const resolvedMdxOptions = applyDefaultOptions({
 					options: partialMdxOptions,
 					defaults: markdownConfigToMdxOptions(
 						extendMarkdownConfig ? config.markdown : markdownConfigDefaults
 					),
 				});
 
-				updateConfig({
-					vite: {
-						plugins: [vitePluginMdx(mdxOptions), vitePluginMdxPostprocess(config)],
-					},
-				});
+				// Mutate `mdxOptions` so that `vitePluginMdx` can reference the actual options
+				Object.assign(mdxOptions, resolvedMdxOptions);
+				// @ts-expect-error After we assign, we don't need to reference `mdxOptions` in this context anymore.
+				// Re-assign it so that the garbage can be collected later.
+				mdxOptions = {};
 			},
 		},
 	};
@@ -81,7 +94,8 @@ export default function mdx(partialMdxOptions: Partial<MdxOptions> = {}): AstroI
 const defaultMdxOptions = {
 	extendMarkdownConfig: true,
 	recmaPlugins: [],
-};
+	optimize: false,
+} satisfies Partial<MdxOptions>;
 
 function markdownConfigToMdxOptions(markdownConfig: typeof markdownConfigDefaults): MdxOptions {
 	return {
@@ -90,7 +104,6 @@ function markdownConfigToMdxOptions(markdownConfig: typeof markdownConfigDefault
 		remarkPlugins: ignoreStringPlugins(markdownConfig.remarkPlugins),
 		rehypePlugins: ignoreStringPlugins(markdownConfig.rehypePlugins),
 		remarkRehype: (markdownConfig.remarkRehype as any) ?? {},
-		optimize: false,
 	};
 }
 
diff --git a/packages/integrations/mdx/src/vite-plugin-mdx.ts b/packages/integrations/mdx/src/vite-plugin-mdx.ts
index 4d3479129238..1b966ecd2a30 100644
--- a/packages/integrations/mdx/src/vite-plugin-mdx.ts
+++ b/packages/integrations/mdx/src/vite-plugin-mdx.ts
@@ -17,6 +17,10 @@ export function vitePluginMdx(mdxOptions: MdxOptions): Plugin {
 			processor = undefined;
 		},
 		configResolved(resolved) {
+			// `mdxOptions` should be populated at this point, but `astro sync` doesn't call `astro:config:done` :(
+			// Workaround this for now by skipping here. `astro sync` shouldn't call the `transform()` hook here anyways.
+			if (Object.keys(mdxOptions).length === 0) return;
+
 			processor = createMdxProcessor(mdxOptions, {
 				sourcemap: !!resolved.build.sourcemap,
 			});
diff --git a/packages/integrations/mdx/test/mdx-plugins.test.js b/packages/integrations/mdx/test/mdx-plugins.test.js
index 6b15884fb712..06e4cc3ad654 100644
--- a/packages/integrations/mdx/test/mdx-plugins.test.js
+++ b/packages/integrations/mdx/test/mdx-plugins.test.js
@@ -64,6 +64,30 @@ describe('MDX plugins', () => {
 		assert.notEqual(selectRehypeExample(document), null);
 	});
 
+	it('supports custom rehype plugins from integrations', async () => {
+		const fixture = await buildFixture({
+			integrations: [
+				mdx(),
+				{
+					name: 'test',
+					hooks: {
+						'astro:config:setup': ({ updateConfig }) => {
+							updateConfig({
+								markdown: {
+									rehypePlugins: [rehypeExamplePlugin],
+								}
+							});
+						}
+					}
+				}
+			],
+		});
+		const html = await fixture.readFile(FILE);
+		const { document } = parseHTML(html);
+
+		assert.notEqual(selectRehypeExample(document), null);
+	});
+
 	it('supports custom rehype plugins with namespaced attributes', async () => {
 		const fixture = await buildFixture({
 			integrations: [