diff --git a/CHANGELOG.md b/CHANGELOG.md
index 684a2775e1f6..78f4c2df9e23 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix issue with `@apply` not working as expected with `!important` inside an atrule ([#2824](https://github.com/tailwindlabs/tailwindcss/pull/2824))
 - Fix issue with `@apply` not working as expected with defined classes ([#2832](https://github.com/tailwindlabs/tailwindcss/pull/2832))
+- Fix memory leak, and broken `@apply` when splitting up files ([#3032](https://github.com/tailwindlabs/tailwindcss/pull/3032))
 
 ### Added
 
diff --git a/__tests__/applyAtRule.test.js b/__tests__/applyAtRule.test.js
index 13f7b8ef907f..3cf53394c26d 100644
--- a/__tests__/applyAtRule.test.js
+++ b/__tests__/applyAtRule.test.js
@@ -337,16 +337,17 @@ test('you can apply utility classes that do not actually exist as long as they w
   })
 })
 
-test('the shadow lookup is only used if no @tailwind rules were in the source tree', () => {
+test('shadow lookup will be constructed when we have missing @tailwind atrules', () => {
   const input = `
     @tailwind base;
+
     .foo { @apply mt-4; }
   `
 
   expect.assertions(1)
 
-  return run(input).catch((e) => {
-    expect(e).toMatchObject({ name: 'CssSyntaxError' })
+  return run(input).then((result) => {
+    expect(result.css).toContain(`.foo { margin-top: 1rem;\n}`)
   })
 })
 
@@ -1362,3 +1363,40 @@ test('declarations within a rule that uses @apply with !important remain not !im
     expect(result.warnings().length).toBe(0)
   })
 })
+
+test('lookup tree is correctly cached based on used tailwind atrules', async () => {
+  const input1 = `
+    @tailwind utilities;
+
+    .foo { @apply mt-4; }
+  `
+
+  const input2 = `
+    @tailwind components;
+
+    .foo { @apply mt-4; }
+  `
+
+  let config = {
+    corePlugins: [],
+    plugins: [
+      function ({ addUtilities, addComponents }) {
+        addUtilities({ '.mt-4': { marginTop: '1rem' } }, [])
+        addComponents({ '.container': { maxWidth: '500px' } }, [])
+      },
+    ],
+  }
+
+  let output1 = await run(input1, config)
+  let output2 = await run(input2, config)
+
+  expect(output1.css).toMatchCss(`
+    .mt-4 { margin-top: 1rem; }
+    .foo { margin-top: 1rem; }
+  `)
+
+  expect(output2.css).toMatchCss(`
+    .container { max-width: 500px; }
+    .foo { margin-top: 1rem; }
+  `)
+})
diff --git a/perf/tailwind.config.js b/perf/tailwind.config.js
index 7fb2125aae9e..5211607402b6 100644
--- a/perf/tailwind.config.js
+++ b/perf/tailwind.config.js
@@ -1,14 +1,12 @@
+let colors = require('../colors')
 module.exports = {
-  future: 'all',
-  experimental: 'all',
   purge: [],
+  darkMode: 'class',
   theme: {
-    extend: {},
+    extend: { colors },
   },
   variants: [
     'responsive',
-    'motion-safe',
-    'motion-reduce',
     'group-hover',
     'group-focus',
     'hover',
@@ -19,10 +17,6 @@ module.exports = {
     'visited',
     'disabled',
     'checked',
-    'first',
-    'last',
-    'odd',
-    'even',
   ],
   plugins: [],
 }
diff --git a/src/lib/substituteClassApplyAtRules.js b/src/lib/substituteClassApplyAtRules.js
index 7c7c89adc88d..90a3e4544206 100644
--- a/src/lib/substituteClassApplyAtRules.js
+++ b/src/lib/substituteClassApplyAtRules.js
@@ -11,15 +11,25 @@ import substituteScreenAtRules from './substituteScreenAtRules'
 import prefixSelector from '../util/prefixSelector'
 import { useMemo } from '../util/useMemo'
 
-function hasAtRule(css, atRule) {
-  let foundAtRule = false
-
-  css.walkAtRules(atRule, () => {
-    foundAtRule = true
-    return false
-  })
+function hasAtRule(css, atRule, condition) {
+  let found = false
+
+  css.walkAtRules(
+    atRule,
+    condition === undefined
+      ? () => {
+          found = true
+          return false
+        }
+      : (node) => {
+          if (condition(node)) {
+            found = true
+            return false
+          }
+        }
+  )
 
-  return foundAtRule
+  return found
 }
 
 function cloneWithoutChildren(node) {
@@ -298,7 +308,7 @@ function processApplyAtRules(css, lookupTree, config) {
   return css
 }
 
-let defaultTailwindTree = null
+let defaultTailwindTree = new Map()
 
 export default function substituteClassApplyAtRules(config, getProcessedPlugins, configChanged) {
   return function (css) {
@@ -307,15 +317,29 @@ export default function substituteClassApplyAtRules(config, getProcessedPlugins,
       return css
     }
 
-    // Tree already contains @tailwind rules, don't prepend default Tailwind tree
-    if (hasAtRule(css, 'tailwind')) {
+    let requiredTailwindAtRules = ['base', 'components', 'utilities']
+    if (
+      hasAtRule(css, 'tailwind', (node) => {
+        let idx = requiredTailwindAtRules.indexOf(node.params)
+        if (idx !== -1) requiredTailwindAtRules.splice(idx, 1)
+        if (requiredTailwindAtRules.length <= 0) return true
+        return false
+      })
+    ) {
+      // Tree already contains all the at rules (requiredTailwindAtRules)
       return processApplyAtRules(css, postcss.root(), config)
     }
 
-    // Tree contains no @tailwind rules, so generate all of Tailwind's styles and
-    // prepend them to the user's CSS. Important for <style> blocks in Vue components.
+    let lookupKey = requiredTailwindAtRules.join(',')
+
+    // We mutated the `requiredTailwindAtRules`, but when we hit this point in
+    // time, it means that we don't have all the atrules. The missing atrules
+    // are listed inside the requiredTailwindAtRules, which we can use to fill
+    // in the missing pieces.
+    //
+    // Important for <style> blocks in Vue components.
     const generateLookupTree =
-      configChanged || defaultTailwindTree === null
+      configChanged || !defaultTailwindTree.has(lookupKey)
         ? () => {
             return postcss([
               substituteTailwindAtRules(config, getProcessedPlugins()),
@@ -325,20 +349,15 @@ export default function substituteClassApplyAtRules(config, getProcessedPlugins,
               convertLayerAtRulesToControlComments(config),
               substituteScreenAtRules(config),
             ])
-              .process(
-                `
-                  @tailwind base;
-                  @tailwind components;
-                  @tailwind utilities;
-                `,
-                { from: undefined }
-              )
+              .process(requiredTailwindAtRules.map((rule) => `@tailwind ${rule};`).join('\n'), {
+                from: undefined,
+              })
               .then((result) => {
-                defaultTailwindTree = result
-                return defaultTailwindTree
+                defaultTailwindTree.set(lookupKey, result)
+                return result
               })
           }
-        : () => Promise.resolve(defaultTailwindTree)
+        : () => Promise.resolve(defaultTailwindTree.get(lookupKey))
 
     return generateLookupTree().then((result) => {
       return processApplyAtRules(css, result.root, config)
diff --git a/src/processTailwindFeatures.js b/src/processTailwindFeatures.js
index 2ab557ca15a1..76b335fddd1c 100644
--- a/src/processTailwindFeatures.js
+++ b/src/processTailwindFeatures.js
@@ -18,6 +18,7 @@ import { issueFlagNotices } from './featureFlags.js'
 
 import hash from 'object-hash'
 import log from './util/log'
+import { shared } from './util/disposables'
 
 let previousConfig = null
 let processedPlugins = null
@@ -30,6 +31,7 @@ export default function (getConfig) {
     previousConfig = config
 
     if (configChanged) {
+      shared.dispose()
       if (config.target) {
         log.warn([
           'The `target` feature has been removed in Tailwind CSS v2.0.',
diff --git a/src/util/disposables.js b/src/util/disposables.js
new file mode 100644
index 000000000000..46b61758609b
--- /dev/null
+++ b/src/util/disposables.js
@@ -0,0 +1,22 @@
+export function disposables() {
+  let disposables = []
+
+  let api = {
+    add(cb) {
+      disposables.push(cb)
+
+      return () => {
+        let idx = disposables.indexOf(cb)
+        if (idx !== -1) disposables.splice(idx, 1)
+      }
+    },
+    dispose() {
+      disposables.splice(0).forEach((dispose) => dispose())
+    },
+  }
+
+  return api
+}
+
+// A shared disposables collection
+export let shared = disposables()
diff --git a/src/util/useMemo.js b/src/util/useMemo.js
index a70c397f05fb..e050c9e48b06 100644
--- a/src/util/useMemo.js
+++ b/src/util/useMemo.js
@@ -1,14 +1,23 @@
+import { shared } from './disposables'
+
 export function useMemo(cb, keyResolver) {
-  const cache = new Map()
+  let cache = new Map()
+
+  function clearCache() {
+    cache.clear()
+    shared.add(clearCache)
+  }
+
+  shared.add(clearCache)
 
   return (...args) => {
-    const key = keyResolver(...args)
+    let key = keyResolver(...args)
 
     if (cache.has(key)) {
       return cache.get(key)
     }
 
-    const result = cb(...args)
+    let result = cb(...args)
     cache.set(key, result)
 
     return result