diff --git a/CHANGELOG.md b/CHANGELOG.md
index 35eb85fd2bea..9c1cca3bb545 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - _Upgrade (experimental)_: Ignore analyzing imports with external URLs (e.g.: `@import "https://fonts.google.com"`) ([#15040](https://github.com/tailwindlabs/tailwindcss/pull/15040))
 - _Upgrade (experimental)_: Ignore analyzing imports with `url(…)` (e.g.: `@import url("https://fonts.google.com")`) ([#15040](https://github.com/tailwindlabs/tailwindcss/pull/15040))
 - _Upgrade (experimental)_: Use `resolveJsId` when resolving `tailwindcss/package.json` ([#15041](https://github.com/tailwindlabs/tailwindcss/pull/15041))
+- _Upgrade (experimental)_: Ensure children of Tailwind root file are not considered Tailwind root files ([#15048](https://github.com/tailwindlabs/tailwindcss/pull/15048))
 
 ### Changed
 
diff --git a/integrations/upgrade/index.test.ts b/integrations/upgrade/index.test.ts
index 1e39992b96f2..f4dbb2ad2c5a 100644
--- a/integrations/upgrade/index.test.ts
+++ b/integrations/upgrade/index.test.ts
@@ -1970,6 +1970,107 @@ test(
   },
 )
 
+test(
+  'finds the correct root Tailwind CSS file',
+  {
+    fs: {
+      'package.json': json`
+        {
+          "dependencies": {
+            "tailwindcss": "^3",
+            "@tailwindcss/upgrade": "workspace:^"
+          }
+        }
+      `,
+      'tailwind.config.ts': js`export default {}`,
+
+      /* Considered a Tailwind root because of: `@import 'tailwindcss/components'` */
+      'src/index.css': css`
+        @import 'base.css';
+        @import 'other.css';
+        @import 'tailwindcss/components';
+        @import 'utilities.css';
+      `,
+
+      /* Considered a Tailwind root because of: `@tailwind base` */
+      'src/base.css': css`
+        html {
+          color: red;
+        }
+        @tailwind base;
+      `,
+      'src/other.css': css`
+        .typography {
+          color: red;
+        }
+      `,
+
+      /* Considered a Tailwind root because of: `@tailwind utilities` */
+      'src/utilities.css': css`
+        @layer utilities {
+          .foo {
+            color: red;
+          }
+        }
+
+        @tailwind utilities;
+      `,
+    },
+  },
+  async ({ exec, fs }) => {
+    await exec('npx @tailwindcss/upgrade --force')
+
+    expect(await fs.dumpFiles('./src/**/*.{html,css}')).toMatchInlineSnapshot(`
+      "
+      --- ./src/index.css ---
+      @import './base.css' layer(components);
+      @import './other.css' layer(components);
+      @import './utilities.css';
+
+      --- ./src/base.css ---
+      @import 'tailwindcss/theme' layer(theme);
+      @import 'tailwindcss/preflight' layer(base);
+
+      /*
+        The default border color has changed to \`currentColor\` in Tailwind CSS v4,
+        so we've added these compatibility styles to make sure everything still
+        looks the same as it did with Tailwind CSS v3.
+
+        If we ever want to remove these styles, we need to add an explicit border
+        color utility to any element that depends on these defaults.
+      */
+      @layer base {
+        *,
+        ::after,
+        ::before,
+        ::backdrop,
+        ::file-selector-button {
+          border-color: var(--color-gray-200, currentColor);
+        }
+      }
+
+      @layer base {
+        html {
+          color: red;
+        }
+      }
+
+      --- ./src/other.css ---
+      .typography {
+        color: red;
+      }
+
+      --- ./src/utilities.css ---
+      @import 'tailwindcss/utilities' layer(utilities);
+
+      @utility foo {
+        color: red;
+      }
+      "
+    `)
+  },
+)
+
 test(
   'relative imports without a relative path prefix are migrated to include a relative path prefix',
   {
diff --git a/packages/@tailwindcss-upgrade/src/migrate.ts b/packages/@tailwindcss-upgrade/src/migrate.ts
index 08aad4c46716..1e6af335ab5d 100644
--- a/packages/@tailwindcss-upgrade/src/migrate.ts
+++ b/packages/@tailwindcss-upgrade/src/migrate.ts
@@ -282,10 +282,10 @@ export async function analyze(stylesheets: Stylesheet[]) {
       // parent A and parent B will be moved to the parent of parent A and
       // parent B. Parent A and parent B will be removed.
       let repeat = true
-      while (repeat) {
+      repeat: while (repeat) {
         repeat = false
 
-        outer: for (let [sheetA, childrenA] of commonParents) {
+        for (let [sheetA, childrenA] of commonParents) {
           for (let [sheetB, childrenB] of commonParents) {
             if (sheetA === sheetB) continue
 
@@ -316,12 +316,11 @@ export async function analyze(stylesheets: Stylesheet[]) {
                   commonParents.get(parent).add(child)
                 }
 
-                repeat = parent !== sheetA && parent !== sheetB
-
                 // Found a common parent between sheet A and sheet B. We can
                 // stop looking for more common parents between A and B, and
                 // continue with the next sheet.
-                break outer
+                repeat = true
+                continue repeat
               }
             }
           }