diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6922f5bfd3eb..108fc3a26274 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add new `shadow-initial` and `inset-shadow-initial` utilities for resetting shadow colors ([#14468](https://github.com/tailwindlabs/tailwindcss/pull/14468))
 - Add `field-sizing-*` utilities ([#14469](https://github.com/tailwindlabs/tailwindcss/pull/14469))
 - Include gradient color properties in color transitions ([#14489](https://github.com/tailwindlabs/tailwindcss/pull/14489))
-- _Experimental_: Add CSS codemods for migrating `@tailwind` directives ([#14411](https://github.com/tailwindlabs/tailwindcss/pull/14411))
+- _Experimental_: Add CSS codemods for `@apply` ([#14411](https://github.com/tailwindlabs/tailwindcss/pull/14434))
+- _Experimental_: Add CSS codemods for migrating `@tailwind` directives ([#14411](https://github.com/tailwindlabs/tailwindcss/pull/14411), [#14504](https://github.com/tailwindlabs/tailwindcss/pull/14504))
 - _Experimental_: Add CSS codemods for migrating `@layer utilities` and `@layer components` ([#14455](https://github.com/tailwindlabs/tailwindcss/pull/14455))
 
 ### Fixed
diff --git a/integrations/cli/upgrade.test.ts b/integrations/cli/upgrade.test.ts
index 72b1bf4a8a2f..9629a685eb1e 100644
--- a/integrations/cli/upgrade.test.ts
+++ b/integrations/cli/upgrade.test.ts
@@ -65,7 +65,17 @@ test(
       `,
       'src/index.css': css`
         @tailwind base;
+
+        html {
+          color: #333;
+        }
+
         @tailwind components;
+
+        .btn {
+          color: red;
+        }
+
         @tailwind utilities;
       `,
     },
@@ -73,7 +83,27 @@ test(
   async ({ fs, exec }) => {
     await exec('npx @tailwindcss/upgrade')
 
-    await fs.expectFileToContain('src/index.css', css` @import 'tailwindcss'; `)
+    await fs.expectFileToContain('src/index.css', css`@import 'tailwindcss';`)
+    await fs.expectFileToContain(
+      'src/index.css',
+      css`
+        @layer base {
+          html {
+            color: #333;
+          }
+        }
+      `,
+    )
+    await fs.expectFileToContain(
+      'src/index.css',
+      css`
+        @layer components {
+          .btn {
+            color: red;
+          }
+        }
+      `,
+    )
   },
 )
 
diff --git a/packages/@tailwindcss-upgrade/src/codemods/format-nodes.test.ts b/packages/@tailwindcss-upgrade/src/codemods/format-nodes.test.ts
new file mode 100644
index 000000000000..517c517c0cad
--- /dev/null
+++ b/packages/@tailwindcss-upgrade/src/codemods/format-nodes.test.ts
@@ -0,0 +1,35 @@
+import postcss, { type Plugin } from 'postcss'
+import { expect, it } from 'vitest'
+import { formatNodes } from './format-nodes'
+
+function markPretty(): Plugin {
+  return {
+    postcssPlugin: '@tailwindcss/upgrade/mark-pretty',
+    OnceExit(root) {
+      root.walkAtRules('utility', (atRule) => {
+        atRule.raws.tailwind_pretty = true
+      })
+    },
+  }
+}
+
+function migrate(input: string) {
+  return postcss()
+    .use(markPretty())
+    .use(formatNodes())
+    .process(input, { from: expect.getState().testPath })
+    .then((result) => result.css)
+}
+
+it('should format PostCSS nodes that are marked with tailwind_pretty', async () => {
+  expect(
+    await migrate(`
+      @utility .foo { .foo { color: red; } }`),
+  ).toMatchInlineSnapshot(`
+    "@utility .foo {
+      .foo {
+        color: red;
+      }
+    }"
+  `)
+})
diff --git a/packages/@tailwindcss-upgrade/src/codemods/format-nodes.ts b/packages/@tailwindcss-upgrade/src/codemods/format-nodes.ts
new file mode 100644
index 000000000000..e90e0e2637ca
--- /dev/null
+++ b/packages/@tailwindcss-upgrade/src/codemods/format-nodes.ts
@@ -0,0 +1,30 @@
+import { parse, type ChildNode, type Plugin, type Root } from 'postcss'
+import { format } from 'prettier'
+import { walk, WalkAction } from '../utils/walk'
+
+// Prettier is used to generate cleaner output, but it's only used on the nodes
+// that were marked as `pretty` during the migration.
+export function formatNodes(): Plugin {
+  async function migrate(root: Root) {
+    // Find the nodes to format
+    let nodesToFormat: ChildNode[] = []
+    walk(root, (child) => {
+      if (child.raws.tailwind_pretty) {
+        nodesToFormat.push(child)
+        return WalkAction.Skip
+      }
+    })
+
+    // Format the nodes
+    await Promise.all(
+      nodesToFormat.map(async (node) => {
+        node.replaceWith(parse(await format(node.toString(), { parser: 'css', semi: true })))
+      }),
+    )
+  }
+
+  return {
+    postcssPlugin: '@tailwindcss/upgrade/format-nodes',
+    OnceExit: migrate,
+  }
+}
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-apply.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-apply.ts
index 41ff03ec3323..ebea30e96d6a 100644
--- a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-apply.ts
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-apply.ts
@@ -13,7 +13,6 @@ export function migrateAtApply(): Plugin {
     let params = utilities.map((part) => {
       // Keep whitespace
       if (part.trim() === '') return part
-
       let variants = segment(part, ':')
       let utility = variants.pop()!
 
@@ -36,8 +35,8 @@ export function migrateAtApply(): Plugin {
 
   return {
     postcssPlugin: '@tailwindcss/upgrade/migrate-at-apply',
-    AtRule: {
-      apply: migrate,
+    OnceExit(root) {
+      root.walkAtRules('apply', migrate)
     },
   }
 }
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.test.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.test.ts
index a493639f2ea3..6f1a03301f93 100644
--- a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.test.ts
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.test.ts
@@ -1,6 +1,7 @@
 import dedent from 'dedent'
 import postcss from 'postcss'
 import { describe, expect, it } from 'vitest'
+import { formatNodes } from './format-nodes'
 import { migrateAtLayerUtilities } from './migrate-at-layer-utilities'
 
 const css = dedent
@@ -8,6 +9,7 @@ const css = dedent
 function migrate(input: string) {
   return postcss()
     .use(migrateAtLayerUtilities())
+    .use(formatNodes())
     .process(input, { from: expect.getState().testPath })
     .then((result) => result.css)
 }
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.ts
index 2bc0c9601cbf..c1e383ef5356 100644
--- a/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.ts
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-at-layer-utilities.ts
@@ -1,65 +1,16 @@
-import { AtRule, parse, Rule, type ChildNode, type Comment, type Plugin } from 'postcss'
+import { type AtRule, type Comment, type Plugin, type Rule } from 'postcss'
 import SelectorParser from 'postcss-selector-parser'
-import { format } from 'prettier'
 import { segment } from '../../../tailwindcss/src/utils/segment'
-
-enum WalkAction {
-  // Continue walking the tree. Default behavior.
-  Continue,
-
-  // Skip walking into the current node.
-  Skip,
-
-  // Stop walking the tree entirely.
-  Stop,
-}
-
-interface Walkable<T> {
-  each(cb: (node: T, index: number) => void): void
-}
-
-// Custom walk implementation where we can skip going into nodes when we don't
-// need to process them.
-function walk<T>(rule: Walkable<T>, cb: (rule: T) => void | WalkAction): undefined | false {
-  let result: undefined | false = undefined
-
-  rule.each?.((node) => {
-    let action = cb(node) ?? WalkAction.Continue
-    if (action === WalkAction.Stop) {
-      result = false
-      return result
-    }
-    if (action !== WalkAction.Skip) {
-      result = walk(node as Walkable<T>, cb)
-      return result
-    }
-  })
-
-  return result
-}
-
-// Depth first walk reversal implementation.
-function walkDepth<T>(rule: Walkable<T>, cb: (rule: T) => void) {
-  rule?.each?.((node) => {
-    walkDepth(node as Walkable<T>, cb)
-    cb(node)
-  })
-}
+import { walk, WalkAction, walkDepth } from '../utils/walk'
 
 export function migrateAtLayerUtilities(): Plugin {
   function migrate(atRule: AtRule) {
     // Only migrate `@layer utilities` and `@layer components`.
     if (atRule.params !== 'utilities' && atRule.params !== 'components') return
 
-    // If the `@layer utilities` contains CSS that should not be turned into an
-    // `@utility` at-rule, then we have to keep it around (including the
-    // `@layer utilities` wrapper). To prevent this from being processed over
-    // and over again, we mark it as seen and bail early.
-    if (atRule.raws.seen) return
-
     // Keep rules that should not be turned into utilities as is. This will
     // include rules with element or ID selectors.
-    let defaultsAtRule = atRule.clone({ raws: { seen: true } })
+    let defaultsAtRule = atRule.clone()
 
     // Clone each rule with multiple selectors into their own rule with a single
     // selector.
@@ -312,32 +263,12 @@ export function migrateAtLayerUtilities(): Plugin {
 
   return {
     postcssPlugin: '@tailwindcss/upgrade/migrate-at-layer-utilities',
-    OnceExit: async (root) => {
+    OnceExit: (root) => {
       // Migrate `@layer utilities` and `@layer components` into `@utility`.
       // Using this instead of the visitor API in case we want to use
       // postcss-nesting in the future.
       root.walkAtRules('layer', migrate)
 
-      // Prettier is used to generate cleaner output, but it's only used on the
-      // nodes that were marked as `pretty` during the migration.
-      {
-        // Find the nodes to format
-        let nodesToFormat: ChildNode[] = []
-        walk(root, (child) => {
-          if (child.raws.tailwind_pretty) {
-            nodesToFormat.push(child)
-            return WalkAction.Skip
-          }
-        })
-
-        // Format the nodes
-        await Promise.all(
-          nodesToFormat.map(async (node) => {
-            node.replaceWith(parse(await format(node.toString(), { parser: 'css', semi: true })))
-          }),
-        )
-      }
-
       // Merge `@utility <name>` with the same name into a single rule. This can
       // happen when the same classes is used in multiple `@layer utilities`
       // blocks.
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.test.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.test.ts
new file mode 100644
index 000000000000..c33bcc03e1d3
--- /dev/null
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.test.ts
@@ -0,0 +1,65 @@
+import dedent from 'dedent'
+import postcss from 'postcss'
+import { expect, it } from 'vitest'
+import { formatNodes } from './format-nodes'
+import { migrateMissingLayers } from './migrate-missing-layers'
+
+const css = dedent
+
+function migrate(input: string) {
+  return postcss()
+    .use(migrateMissingLayers())
+    .use(formatNodes())
+    .process(input, { from: expect.getState().testPath })
+    .then((result) => result.css)
+}
+
+it('should migrate rules between tailwind directives', async () => {
+  expect(
+    await migrate(css`
+      @tailwind base;
+
+      .base {
+      }
+
+      @tailwind components;
+
+      .component-a {
+      }
+      .component-b {
+      }
+
+      @tailwind utilities;
+
+      .utility-a {
+      }
+      .utility-b {
+      }
+    `),
+  ).toMatchInlineSnapshot(`
+    "@tailwind base;
+
+    @layer base {
+      .base {
+      }
+    }
+
+    @tailwind components;
+
+    @layer components {
+      .component-a {
+      }
+      .component-b {
+      }
+    }
+
+    @tailwind utilities;
+
+    @layer utilities {
+      .utility-a {
+      }
+      .utility-b {
+      }
+    }"
+  `)
+})
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.ts
new file mode 100644
index 000000000000..3c1818ff24a4
--- /dev/null
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-missing-layers.ts
@@ -0,0 +1,110 @@
+import { AtRule, type ChildNode, type Plugin, type Root } from 'postcss'
+
+export function migrateMissingLayers(): Plugin {
+  function migrate(root: Root) {
+    let lastLayer = ''
+    let bucket: ChildNode[] = []
+    let buckets: [layer: string, bucket: typeof bucket][] = []
+
+    root.each((node) => {
+      if (node.type === 'atrule') {
+        // Known Tailwind directives that should not be inside a layer.
+        if (node.name === 'theme' || node.name === 'utility') {
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+          return
+        }
+
+        // Base
+        if (
+          (node.name === 'tailwind' && node.params === 'base') ||
+          (node.name === 'import' && node.params.match(/^["']tailwindcss\/base["']/))
+        ) {
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+
+          lastLayer = 'base'
+          return
+        }
+
+        // Components
+        if (
+          (node.name === 'tailwind' && node.params === 'components') ||
+          (node.name === 'import' && node.params.match(/^["']tailwindcss\/components["']/))
+        ) {
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+
+          lastLayer = 'components'
+          return
+        }
+
+        // Utilities
+        if (
+          (node.name === 'tailwind' && node.params === 'utilities') ||
+          (node.name === 'import' && node.params.match(/^["']tailwindcss\/utilities["']/))
+        ) {
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+
+          lastLayer = 'utilities'
+          return
+        }
+
+        // Already in a layer
+        if (node.name === 'layer') {
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+          return
+        }
+
+        // Add layer to `@import` at-rules
+        if (node.name === 'import') {
+          if (!node.params.includes('layer(')) {
+            node.params += ` layer(${lastLayer})`
+          }
+
+          if (bucket.length > 0) {
+            buckets.push([lastLayer, bucket.splice(0)])
+          }
+          return
+        }
+      }
+
+      // Track the node
+      if (lastLayer !== '') {
+        if (bucket.push(node) !== 1) {
+          node.remove()
+        }
+      }
+    })
+
+    // Add the last bucket if it's not empty
+    if (bucket.length > 0) {
+      buckets.push([lastLayer, bucket.splice(0)])
+    }
+
+    // Wrap each bucket in an `@layer` at-rule
+    for (let [layerName, nodes] of buckets) {
+      let layerNode = new AtRule({
+        name: 'layer',
+        params: layerName,
+        nodes,
+        raws: {
+          tailwind_pretty: true,
+        },
+      })
+      nodes[0].replaceWith(layerNode)
+    }
+  }
+
+  return {
+    postcssPlugin: '@tailwindcss/upgrade/migrate-missing-layers',
+    OnceExit: migrate,
+  }
+}
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.test.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.test.ts
index f59fef01e848..9f4ae095501d 100644
--- a/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.test.ts
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.test.ts
@@ -1,6 +1,7 @@
 import dedent from 'dedent'
 import postcss from 'postcss'
 import { expect, it } from 'vitest'
+import { formatNodes } from './format-nodes'
 import { migrateTailwindDirectives } from './migrate-tailwind-directives'
 
 const css = dedent
@@ -8,6 +9,7 @@ const css = dedent
 function migrate(input: string) {
   return postcss()
     .use(migrateTailwindDirectives())
+    .use(formatNodes())
     .process(input, { from: expect.getState().testPath })
     .then((result) => result.css)
 }
diff --git a/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.ts b/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.ts
index cb47714a0197..5bb4a34e2349 100644
--- a/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.ts
+++ b/packages/@tailwindcss-upgrade/src/codemods/migrate-tailwind-directives.ts
@@ -86,6 +86,6 @@ export function migrateTailwindDirectives(): Plugin {
 
   return {
     postcssPlugin: '@tailwindcss/upgrade/migrate-tailwind-directives',
-    Once: migrate,
+    OnceExit: migrate,
   }
 }
diff --git a/packages/@tailwindcss-upgrade/src/index.test.ts b/packages/@tailwindcss-upgrade/src/index.test.ts
index a043092d9ae6..2f4f7475e3f6 100644
--- a/packages/@tailwindcss-upgrade/src/index.test.ts
+++ b/packages/@tailwindcss-upgrade/src/index.test.ts
@@ -26,3 +26,95 @@ it('should print the input as-is', async () => {
     }"
   `)
 })
+
+it('should migrate a stylesheet', async () => {
+  expect(
+    await migrateContents(css`
+      @tailwind base;
+
+      html {
+        overflow: hidden;
+      }
+
+      @tailwind components;
+
+      .a {
+        z-index: 1;
+      }
+
+      @layer components {
+        .b {
+          z-index: 2;
+        }
+      }
+
+      .c {
+        z-index: 3;
+      }
+
+      @tailwind utilities;
+
+      .d {
+        z-index: 4;
+      }
+
+      @layer utilities {
+        .e {
+          z-index: 5;
+        }
+      }
+    `),
+  ).toMatchInlineSnapshot(`
+    "@import 'tailwindcss';
+
+    @layer base {
+      html {
+        overflow: hidden;
+      }
+    }
+
+    @layer components {
+      .a {
+        z-index: 1;
+      }
+    }
+
+    @utility b {
+      z-index: 2;
+    }
+
+    @layer components {
+      .c {
+        z-index: 3;
+      }
+    }
+
+    @layer utilities {
+      .d {
+        z-index: 4;
+      }
+    }
+
+    @utility e {
+      z-index: 5;
+    }"
+  `)
+})
+
+it('should migrate a stylesheet (with imports)', async () => {
+  expect(
+    await migrateContents(css`
+      @import 'tailwindcss/base';
+      @import './my-base.css';
+      @import 'tailwindcss/components';
+      @import './my-components.css';
+      @import 'tailwindcss/utilities';
+      @import './my-utilities.css';
+    `),
+  ).toMatchInlineSnapshot(`
+    "@import 'tailwindcss';
+    @import './my-base.css' layer(base);
+    @import './my-components.css' layer(components);
+    @import './my-utilities.css' layer(utilities);"
+  `)
+})
diff --git a/packages/@tailwindcss-upgrade/src/migrate.ts b/packages/@tailwindcss-upgrade/src/migrate.ts
index 88c54350db5f..cfbe50d3dcb3 100644
--- a/packages/@tailwindcss-upgrade/src/migrate.ts
+++ b/packages/@tailwindcss-upgrade/src/migrate.ts
@@ -1,15 +1,19 @@
 import fs from 'node:fs/promises'
 import path from 'node:path'
 import postcss from 'postcss'
+import { formatNodes } from './codemods/format-nodes'
 import { migrateAtApply } from './codemods/migrate-at-apply'
 import { migrateAtLayerUtilities } from './codemods/migrate-at-layer-utilities'
+import { migrateMissingLayers } from './codemods/migrate-missing-layers'
 import { migrateTailwindDirectives } from './codemods/migrate-tailwind-directives'
 
 export async function migrateContents(contents: string, file?: string) {
   return postcss()
     .use(migrateAtApply())
-    .use(migrateTailwindDirectives())
     .use(migrateAtLayerUtilities())
+    .use(migrateMissingLayers())
+    .use(migrateTailwindDirectives())
+    .use(formatNodes())
     .process(contents, { from: file })
     .then((result) => result.css)
 }
diff --git a/packages/@tailwindcss-upgrade/src/utils/walk.ts b/packages/@tailwindcss-upgrade/src/utils/walk.ts
new file mode 100644
index 000000000000..7a86b7ae533d
--- /dev/null
+++ b/packages/@tailwindcss-upgrade/src/utils/walk.ts
@@ -0,0 +1,42 @@
+export enum WalkAction {
+  // Continue walking the tree. Default behavior.
+  Continue,
+
+  // Skip walking into the current node.
+  Skip,
+
+  // Stop walking the tree entirely.
+  Stop,
+}
+
+interface Walkable<T> {
+  each(cb: (node: T, index: number) => void): void
+}
+
+// Custom walk implementation where we can skip going into nodes when we don't
+// need to process them.
+export function walk<T>(rule: Walkable<T>, cb: (rule: T) => void | WalkAction): undefined | false {
+  let result: undefined | false = undefined
+
+  rule.each?.((node) => {
+    let action = cb(node) ?? WalkAction.Continue
+    if (action === WalkAction.Stop) {
+      result = false
+      return result
+    }
+    if (action !== WalkAction.Skip) {
+      result = walk(node as Walkable<T>, cb)
+      return result
+    }
+  })
+
+  return result
+}
+
+// Depth first walk reversal implementation.
+export function walkDepth<T>(rule: Walkable<T>, cb: (rule: T) => void) {
+  rule?.each?.((node) => {
+    walkDepth(node as Walkable<T>, cb)
+    cb(node)
+  })
+}