diff --git a/packages/tailwindcss/src/compat/config.test.ts b/packages/tailwindcss/src/compat/config.test.ts
index b5e89ad4f..b40abd4e5 100644
--- a/packages/tailwindcss/src/compat/config.test.ts
+++ b/packages/tailwindcss/src/compat/config.test.ts
@@ -195,3 +195,37 @@ test('Config files can affect the theme', async ({ expect }) => {
     "
   `)
 })
+
+test('Variants in CSS overwrite variants from plugins', async ({ expect }) => {
+  let input = css`
+    @tailwind utilities;
+    @config "./config.js";
+    @variant dark (&:is(.my-dark));
+    @variant light (&:is(.my-light));
+  `
+
+  let compiler = await compile(input, {
+    loadConfig: async () => ({
+      darkMode: ['variant', '&:is(.dark)'],
+      plugins: [
+        plugin(function ({ addVariant }) {
+          addVariant('light', '&:is(.light)')
+        }),
+      ],
+    }),
+  })
+
+  expect(compiler.build(['dark:underline', 'light:underline'])).toMatchInlineSnapshot(`
+    ".dark\\:underline {
+      &:is(.my-dark) {
+        text-decoration-line: underline;
+      }
+    }
+    .light\\:underline {
+      &:is(.my-light) {
+        text-decoration-line: underline;
+      }
+    }
+    "
+  `)
+})
diff --git a/packages/tailwindcss/src/compat/merge-into-theme.test.ts b/packages/tailwindcss/src/compat/merge-into-theme.test.ts
new file mode 100644
index 000000000..f5e1606d5
--- /dev/null
+++ b/packages/tailwindcss/src/compat/merge-into-theme.test.ts
@@ -0,0 +1,47 @@
+import { test } from 'vitest'
+import { Theme } from '../theme'
+import { mergeIntoTheme } from './merge-into-theme'
+
+test('Config values can be merged into the theme', ({ expect }) => {
+  let theme = new Theme()
+
+  mergeIntoTheme(theme, {
+    colors: {
+      primary: '#c0ffee',
+      red: {
+        500: 'red',
+      },
+    },
+
+    fontSize: {
+      sm: '0.875rem',
+      base: [
+        '1rem',
+        {
+          lineHeight: '1.5',
+        },
+      ],
+    },
+  })
+
+  expect(theme.resolve('primary', ['--colors'] as any[])).toEqual('#c0ffee')
+  expect(theme.resolve('red-500', ['--colors'] as any[])).toEqual('red')
+  expect(theme.resolve('sm', ['--font-size'] as any[])).toEqual('0.875rem')
+  expect(theme.resolve('base', ['--font-size'] as any[])).toEqual('1rem')
+  expect(theme.get(['--font-size-base--line-height'] as any[])).toEqual('1.5')
+})
+
+test('Existing values are not overwritten', ({ expect }) => {
+  let theme = new Theme()
+  theme.add('--colors-primary', '#c0ffee')
+
+  mergeIntoTheme(theme, {
+    colors: {
+      primary: '#c0ffee',
+      secondary: '#bada55',
+    },
+  })
+
+  expect(theme.resolve('primary', ['--colors'] as any[])).toEqual('var(--colors-primary, #c0ffee)')
+  expect(theme.resolve('secondary', ['--colors'] as any[])).toEqual('#bada55')
+})
diff --git a/packages/tailwindcss/src/compat/merge-into-theme.ts b/packages/tailwindcss/src/compat/merge-into-theme.ts
new file mode 100644
index 000000000..8929db6bf
--- /dev/null
+++ b/packages/tailwindcss/src/compat/merge-into-theme.ts
@@ -0,0 +1,125 @@
+import type { DesignSystem } from '../design-system'
+import { resolveConfig, type ConfigFile } from './config/resolve-config'
+import type { ResolvedConfig } from './config/types'
+
+export function mergeIntoTheme(designSystem: DesignSystem, configs: ConfigFile[]) {
+  let theme = resolveConfig(designSystem, configs).theme
+
+  for (let [path, value] of themeableValues(theme)) {
+    let name = keyPathToCssProperty(path)
+
+    designSystem.theme.add(`--${name}`, value as any, {
+      isInline: true,
+      isReference: false,
+    })
+  }
+
+  return theme
+}
+
+function themeableValues(config: ResolvedConfig['theme']): [string[], unknown][] {
+  let toAdd: [string[], unknown][] = []
+
+  walk(config as any, [], (value, path) => {
+    if (isValidThemePrimitive(value)) {
+      toAdd.push([path, value])
+
+      return WalkAction.Skip
+    }
+
+    if (isValidThemeTuple(value)) {
+      toAdd.push([path, value[0]])
+
+      for (let key of Reflect.ownKeys(value[1]) as string[]) {
+        toAdd.push([[...path, `-${key}`], value[1][key]])
+      }
+
+      return WalkAction.Skip
+    }
+  })
+
+  return toAdd
+}
+
+function keyPathToCssProperty(path: string[]) {
+  return (
+    path
+      // [1] should move into the nested object tuple. To create the CSS variable
+      // name for this, we replace it with an empty string that will result in two
+      // subsequent dashes when joined.
+      .map((path) => (path === '1' ? '' : path))
+
+      // Resolve the key path to a CSS variable segment
+      .map((part) =>
+        part
+          .replaceAll('.', '_')
+          .replace(/([a-z])([A-Z])/g, (_, a, b) => `${a}-${b.toLowerCase()}`),
+      )
+
+      // Remove the `DEFAULT` key at the end of a path
+      // We're reading from CSS anyway so it'll be a string
+      .filter((part, index) => part !== 'DEFAULT' || index !== path.length - 1)
+      .join('-')
+  )
+}
+
+function isValidThemePrimitive(value: unknown) {
+  return typeof value === 'number' || typeof value === 'string'
+}
+
+function isValidThemeTuple(value: unknown): value is [string, Record<string, string | number>] {
+  // Check for tuple values of the form
+  // `[string, Record<string, string | number>]`
+  if (!Array.isArray(value)) return false
+  if (value.length !== 2) return false
+
+  // A string or number as the "value"
+  if (typeof value[0] !== 'string' && typeof value[0] !== 'number') return false
+
+  // An object as the nested theme values
+  if (value[1] === undefined || value[1] === null) return false
+  if (typeof value[1] !== 'object') return false
+
+  for (let key of Reflect.ownKeys(value[1])) {
+    if (typeof key !== 'string') return false
+    if (typeof value[1][key] !== 'string' && typeof value[1][key] !== 'number') return false
+  }
+
+  return true
+}
+
+enum WalkAction {
+  /** Continue walking, which is the default */
+  Continue,
+
+  /** Skip visiting the children of this node */
+  Skip,
+
+  /** Stop the walk entirely */
+  Stop,
+}
+
+function walk(
+  obj: Record<string, unknown>,
+  path: string[] = [],
+  callback: (value: unknown, path: string[]) => WalkAction | void,
+) {
+  for (let key of Reflect.ownKeys(obj) as string[]) {
+    let value = obj[key]
+
+    if (value === undefined || value === null) {
+      continue
+    }
+
+    let keyPath = [...path, key]
+
+    let result = callback(value, keyPath) ?? WalkAction.Continue
+
+    if (result === WalkAction.Skip) continue
+    if (result === WalkAction.Stop) break
+
+    if (!Array.isArray(value) && typeof value !== 'object') continue
+
+    walk(value as any, keyPath, callback)
+  }
+}
diff --git a/packages/tailwindcss/src/plugin-api.ts b/packages/tailwindcss/src/plugin-api.ts
index 18eb92f7c..99324b070 100644
--- a/packages/tailwindcss/src/plugin-api.ts
+++ b/packages/tailwindcss/src/plugin-api.ts
@@ -5,6 +5,7 @@ import { createCompatConfig } from './compat/config/create-compat-config'
 import { resolveConfig, type ConfigFile } from './compat/config/resolve-config'
 import type { ResolvedConfig, UserConfig } from './compat/config/types'
 import { darkModePlugin } from './compat/dark-mode'
+import { mergeIntoTheme } from './compat/merge-into-theme'
 import type { DesignSystem } from './design-system'
 import { createThemeFn } from './theme-fn'
 import { withAlpha, withNegative } from './utilities'
@@ -351,10 +352,11 @@ export function registerPlugins(
   ast: AstNode[],
   configs: ConfigFile[],
 ) {
+  let userConfig = [{ config: { plugins } }, ...configs]
+
   let resolvedConfig = resolveConfig(designSystem, [
     { config: createCompatConfig(designSystem.theme) },
-    ...configs,
-    { config: { plugins } },
+    ...userConfig,
     { config: { plugins: [darkModePlugin] } },
   ])
 
@@ -364,6 +366,10 @@ export function registerPlugins(
     handler(pluginApi)
   }
 
+  // Theme keys don't need to read from the compat config because core plugins
+  // _already_ look through "fallback" theme keys
+  mergeIntoTheme(designSystem, userConfig)
+
   return {
     pluginApi,
     resolvedConfig,