diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5c56a754e..61236b94d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Support TypeScript for `@plugin` and `@config` files ([#14317](https://github.com/tailwindlabs/tailwindcss/pull/14317))
+- Add `default` option to `@theme` to support overriding default theme values from plugins/JS config files ([#14327](https://github.com/tailwindlabs/tailwindcss/pull/14327))
 
 ### Fixed
 
@@ -17,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Ensure CSS `theme()` functions are evaluated in media query ranges with collapsed whitespace ((#14321)[https://github.com/tailwindlabs/tailwindcss/pull/14321])
 - Fix support for Nuxt projects in the Vite plugin (requires Nuxt 3.13.1+) ([#14319](https://github.com/tailwindlabs/tailwindcss/pull/14319))
 - Evaluate theme functions in plugins and JS config files ([#14326](https://github.com/tailwindlabs/tailwindcss/pull/14326))
+- Ensure theme values overridden with `reference` values don't generate stale CSS variables ([#14327](https://github.com/tailwindlabs/tailwindcss/pull/14327))
 
 ## [4.0.0-alpha.21] - 2024-09-02
 
diff --git a/packages/tailwindcss/src/compat/apply-config-to-theme.ts b/packages/tailwindcss/src/compat/apply-config-to-theme.ts
index e62b2b741..325c37118 100644
--- a/packages/tailwindcss/src/compat/apply-config-to-theme.ts
+++ b/packages/tailwindcss/src/compat/apply-config-to-theme.ts
@@ -10,7 +10,8 @@ export function applyConfigToTheme(designSystem: DesignSystem, configs: ConfigFi
 
     designSystem.theme.add(`--${name}`, value as any, {
       isInline: true,
-      isReference: false,
+      isReference: true,
+      isDefault: true,
     })
   }
 
diff --git a/packages/tailwindcss/src/index.test.ts b/packages/tailwindcss/src/index.test.ts
index 9a52d5af4..d4fc57379 100644
--- a/packages/tailwindcss/src/index.test.ts
+++ b/packages/tailwindcss/src/index.test.ts
@@ -1292,6 +1292,215 @@ describe('Parsing themes values from CSS', () => {
       }"
     `)
   })
+
+  test('`default` theme values can be overridden by regular theme values`', async () => {
+    expect(
+      await compileCss(
+        css`
+          @theme {
+            --color-potato: #ac855b;
+          }
+          @theme default {
+            --color-potato: #efb46b;
+          }
+
+          @tailwind utilities;
+        `,
+        ['bg-potato'],
+      ),
+    ).toMatchInlineSnapshot(`
+      ":root {
+        --color-potato: #ac855b;
+      }
+
+      .bg-potato {
+        background-color: var(--color-potato, #ac855b);
+      }"
+    `)
+  })
+
+  test('`default` and `inline` can be used together', async () => {
+    expect(
+      await compileCss(
+        css`
+          @theme default inline {
+            --color-potato: #efb46b;
+          }
+
+          @tailwind utilities;
+        `,
+        ['bg-potato'],
+      ),
+    ).toMatchInlineSnapshot(`
+      ":root {
+        --color-potato: #efb46b;
+      }
+
+      .bg-potato {
+        background-color: #efb46b;
+      }"
+    `)
+  })
+
+  test('`default` and `reference` can be used together', async () => {
+    expect(
+      await compileCss(
+        css`
+          @theme default reference {
+            --color-potato: #efb46b;
+          }
+
+          @tailwind utilities;
+        `,
+        ['bg-potato'],
+      ),
+    ).toMatchInlineSnapshot(`
+      ".bg-potato {
+        background-color: var(--color-potato, #efb46b);
+      }"
+    `)
+  })
+
+  test('`default`, `inline`, and `reference` can be used together', async () => {
+    expect(
+      await compileCss(
+        css`
+          @theme default reference inline {
+            --color-potato: #efb46b;
+          }
+
+          @tailwind utilities;
+        `,
+        ['bg-potato'],
+      ),
+    ).toMatchInlineSnapshot(`
+      ".bg-potato {
+        background-color: #efb46b;
+      }"
+    `)
+  })
+
+  test('`default` can be used in `media(…)`', async () => {
+    expect(
+      await compileCss(
+        css`
+          @media theme() {
+            @theme {
+              --color-potato: #ac855b;
+            }
+          }
+          @media theme(default) {
+            @theme {
+              --color-potato: #efb46b;
+              --color-tomato: tomato;
+            }
+          }
+
+          @tailwind utilities;
+        `,
+        ['bg-potato', 'bg-tomato'],
+      ),
+    ).toMatchInlineSnapshot(`
+      ":root {
+        --color-potato: #ac855b;
+        --color-tomato: tomato;
+      }
+
+      .bg-potato {
+        background-color: var(--color-potato, #ac855b);
+      }
+
+      .bg-tomato {
+        background-color: var(--color-tomato, tomato);
+      }"
+    `)
+  })
+
+  test('`default` theme values can be overridden by plugin theme values', async () => {
+    let { build } = await compile(
+      css`
+        @theme default {
+          --color-red: red;
+        }
+        @theme {
+          --color-orange: orange;
+        }
+        @plugin "my-plugin";
+        @tailwind utilities;
+      `,
+      {
+        loadPlugin: async () => {
+          return plugin(({}) => {}, {
+            theme: {
+              extend: {
+                colors: {
+                  red: 'tomato',
+                  orange: '#f28500',
+                },
+              },
+            },
+          })
+        },
+      },
+    )
+
+    expect(optimizeCss(build(['text-red', 'text-orange'])).trim()).toMatchInlineSnapshot(`
+      ":root {
+        --color-orange: orange;
+      }
+
+      .text-orange {
+        color: var(--color-orange, orange);
+      }
+
+      .text-red {
+        color: tomato;
+      }"
+    `)
+  })
+
+  test('`default` theme values can be overridden by config theme values', async () => {
+    let { build } = await compile(
+      css`
+        @theme default {
+          --color-red: red;
+        }
+        @theme {
+          --color-orange: orange;
+        }
+        @config "./my-config.js";
+        @tailwind utilities;
+      `,
+      {
+        loadConfig: async () => {
+          return {
+            theme: {
+              extend: {
+                colors: {
+                  red: 'tomato',
+                  orange: '#f28500',
+                },
+              },
+            },
+          }
+        },
+      },
+    )
+
+    expect(optimizeCss(build(['text-red', 'text-orange'])).trim()).toMatchInlineSnapshot(`
+      ":root {
+        --color-orange: orange;
+      }
+
+      .text-orange {
+        color: var(--color-orange, orange);
+      }
+
+      .text-red {
+        color: tomato;
+      }"
+    `)
+  })
 })
 
 describe('plugins', () => {
diff --git a/packages/tailwindcss/src/index.ts b/packages/tailwindcss/src/index.ts
index 893e83984..e31a82f22 100644
--- a/packages/tailwindcss/src/index.ts
+++ b/packages/tailwindcss/src/index.ts
@@ -28,16 +28,19 @@ function throwOnConfig(): never {
 function parseThemeOptions(selector: string) {
   let isReference = false
   let isInline = false
+  let isDefault = false
 
   for (let option of segment(selector.slice(6) /* '@theme'.length */, ' ')) {
     if (option === 'reference') {
       isReference = true
     } else if (option === 'inline') {
       isInline = true
+    } else if (option === 'default') {
+      isDefault = true
     }
   }
 
-  return { isReference, isInline }
+  return { isReference, isInline, isDefault }
 }
 
 async function parseCss(
@@ -253,8 +256,8 @@ async function parseCss(
             'Files imported with `@import "…" theme(…)` must only contain `@theme` blocks.',
           )
         }
-        if (child.selector === '@theme') {
-          child.selector = '@theme ' + themeParams
+        if (child.selector === '@theme' || child.selector.startsWith('@theme ')) {
+          child.selector += ' ' + themeParams
           return WalkAction.Skip
         }
       })
@@ -264,7 +267,7 @@ async function parseCss(
 
     if (node.selector !== '@theme' && !node.selector.startsWith('@theme ')) return
 
-    let { isReference, isInline } = parseThemeOptions(node.selector)
+    let { isReference, isInline, isDefault } = parseThemeOptions(node.selector)
 
     // Record all custom properties in the `@theme` declaration
     walk(node.nodes, (child, { replaceWith }) => {
@@ -278,7 +281,7 @@ async function parseCss(
 
       if (child.kind === 'comment') return
       if (child.kind === 'declaration' && child.property.startsWith('--')) {
-        theme.add(child.property, child.value ?? '', { isReference, isInline })
+        theme.add(child.property, child.value ?? '', { isReference, isInline, isDefault })
         return
       }
 
@@ -302,6 +305,33 @@ async function parseCss(
     return WalkAction.Skip
   })
 
+  let designSystem = buildDesignSystem(theme)
+
+  let configs = await Promise.all(
+    configPaths.map(async (configPath) => ({
+      path: configPath,
+      config: await loadConfig(configPath),
+    })),
+  )
+
+  let plugins = await Promise.all(
+    pluginPaths.map(async ([pluginPath, pluginOptions]) => ({
+      path: pluginPath,
+      plugin: await loadPlugin(pluginPath),
+      options: pluginOptions,
+    })),
+  )
+
+  let { pluginApi, resolvedConfig } = registerPlugins(plugins, designSystem, ast, configs)
+
+  for (let customVariant of customVariants) {
+    customVariant(designSystem)
+  }
+
+  for (let customUtility of customUtilities) {
+    customUtility(designSystem)
+  }
+
   // Output final set of theme variables at the position of the first `@theme`
   // rule.
   if (firstThemeRule) {
@@ -340,33 +370,6 @@ async function parseCss(
     firstThemeRule.nodes = nodes
   }
 
-  let designSystem = buildDesignSystem(theme)
-
-  let configs = await Promise.all(
-    configPaths.map(async (configPath) => ({
-      path: configPath,
-      config: await loadConfig(configPath),
-    })),
-  )
-
-  let plugins = await Promise.all(
-    pluginPaths.map(async ([pluginPath, pluginOptions]) => ({
-      path: pluginPath,
-      plugin: await loadPlugin(pluginPath),
-      options: pluginOptions,
-    })),
-  )
-
-  let { pluginApi, resolvedConfig } = registerPlugins(plugins, designSystem, ast, configs)
-
-  for (let customVariant of customVariants) {
-    customVariant(designSystem)
-  }
-
-  for (let customUtility of customUtilities) {
-    customUtility(designSystem)
-  }
-
   // Replace `@apply` rules with the actual utility classes.
   if (css.includes('@apply')) {
     substituteAtApply(ast, designSystem)
diff --git a/packages/tailwindcss/src/theme.ts b/packages/tailwindcss/src/theme.ts
index 178472b96..2a7bdb80e 100644
--- a/packages/tailwindcss/src/theme.ts
+++ b/packages/tailwindcss/src/theme.ts
@@ -2,10 +2,17 @@ import { escape } from './utils/escape'
 
 export class Theme {
   constructor(
-    private values = new Map<string, { value: string; isReference: boolean; isInline: boolean }>(),
+    private values = new Map<
+      string,
+      { value: string; isReference: boolean; isInline: boolean; isDefault: boolean }
+    >(),
   ) {}
 
-  add(key: string, value: string, { isReference = false, isInline = false } = {}): void {
+  add(
+    key: string,
+    value: string,
+    { isReference = false, isInline = false, isDefault = false } = {},
+  ): void {
     if (key.endsWith('-*')) {
       if (value !== 'initial') {
         throw new Error(`Invalid theme value \`${value}\` for namespace \`${key}\``)
@@ -17,10 +24,15 @@ export class Theme {
       }
     }
 
+    if (isDefault) {
+      let existing = this.values.get(key)
+      if (existing && !existing.isDefault) return
+    }
+
     if (value === 'initial') {
       this.values.delete(key)
     } else {
-      this.values.set(key, { value, isReference, isInline })
+      this.values.set(key, { value, isReference, isInline, isDefault })
     }
   }
 
diff --git a/packages/tailwindcss/theme.css b/packages/tailwindcss/theme.css
index 190e51f09..a6de6e84a 100644
--- a/packages/tailwindcss/theme.css
+++ b/packages/tailwindcss/theme.css
@@ -1,4 +1,4 @@
-@theme {
+@theme default {
   /* Defaults */
   --default-transition-duration: 150ms;
   --default-transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1);