diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2b327610b..c84cf0858 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Ensure `@tailwindcss/cli` in `--watch` mode doesn't crash on Windows when `@source` points to a directory that doesn't exist ([#20242](https://github.com/tailwindlabs/tailwindcss/pull/20242))
 - Ensure `@tailwindcss/vite` doesn't crash in Deno v2.8.x when `context.parentURL` is not a valid URL ([#20245](https://github.com/tailwindlabs/tailwindcss/pull/20245))
 - Ensure `@tailwindcss/cli` in `--watch` mode rebuilds when the input CSS file changes in an ignored directory ([#20246](https://github.com/tailwindlabs/tailwindcss/pull/20246))
+- Ensure `@variant` rules generated by `addBase` can use custom variants defined later ([#20247](https://github.com/tailwindlabs/tailwindcss/pull/20247))
 
 ## [4.3.1] - 2026-06-12
 
diff --git a/packages/tailwindcss/src/compat/plugin-api.test.ts b/packages/tailwindcss/src/compat/plugin-api.test.ts
index ff6bdce2f..e3ea3fb07 100644
--- a/packages/tailwindcss/src/compat/plugin-api.test.ts
+++ b/packages/tailwindcss/src/compat/plugin-api.test.ts
@@ -1527,6 +1527,41 @@ describe('addBase', () => {
       "
     `)
   })
+
+  test('@variant inside addBase works with custom variants', async () => {
+    expect(
+      await compileCss(
+        css`
+          @plugin "my-plugin";
+
+          @custom-variant custom (&.custom);
+        `,
+        {
+          loadModule: async () => ({
+            path: '',
+            base: '/root',
+            module: plugin(function ({ addBase }) {
+              addBase({
+                ':root': {
+                  '@variant custom': {
+                    '--x': '1',
+                  },
+                },
+              })
+            }),
+          }),
+        },
+      ),
+    ).toMatchInlineSnapshot(`
+      "
+      @layer base {
+        :root.custom {
+          --x: 1;
+        }
+      }
+      "
+    `)
+  })
 })
 
 describe('addVariant', () => {
diff --git a/packages/tailwindcss/src/compat/plugin-api.ts b/packages/tailwindcss/src/compat/plugin-api.ts
index 20ecb14ae..af6e98d77 100644
--- a/packages/tailwindcss/src/compat/plugin-api.ts
+++ b/packages/tailwindcss/src/compat/plugin-api.ts
@@ -13,12 +13,7 @@ import { escape } from '../utils/escape'
 import { inferDataType } from '../utils/infer-data-type'
 import { segment } from '../utils/segment'
 import { toKeyPath } from '../utils/to-key-path'
-import {
-  compoundsForSelectors,
-  IS_VALID_VARIANT_NAME,
-  substituteAtSlot,
-  substituteAtVariant,
-} from '../variants'
+import { compoundsForSelectors, IS_VALID_VARIANT_NAME, substituteAtSlot } from '../variants'
 import { walk, WalkAction } from '../walk'
 import type { ResolvedConfig, UserConfig } from './config/types'
 import { createThemeFn } from './plugin-functions'
@@ -115,7 +110,6 @@ export function buildPluginApi({
       if (referenceMode) return
       let baseNodes = objectToAst(css)
       featuresRef.current |= substituteFunctions(baseNodes, designSystem)
-      featuresRef.current |= substituteAtVariant(baseNodes, designSystem)
       let rule = atRule('@layer', 'base', baseNodes)
       walk([rule], (node) => {
         node.src = src