diff --git a/CHANGELOG.md b/CHANGELOG.md
index b1206d79aec3..61e89a11d00f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-- Nothing yet!
+### Fixed
+
+- Fix `@apply` in files without `@tailwind` directives ([#6580](https://github.com/tailwindlabs/tailwindcss/pull/6580))
 
 ## [3.0.9] - 2022-01-03
 
diff --git a/src/lib/normalizeTailwindDirectives.js b/src/lib/normalizeTailwindDirectives.js
index 274773051680..a60d217e22a6 100644
--- a/src/lib/normalizeTailwindDirectives.js
+++ b/src/lib/normalizeTailwindDirectives.js
@@ -3,8 +3,13 @@ import log from '../util/log'
 export default function normalizeTailwindDirectives(root) {
   let tailwindDirectives = new Set()
   let layerDirectives = new Set()
+  let applyDirectives = new Set()
 
   root.walkAtRules((atRule) => {
+    if (atRule.name === 'apply') {
+      applyDirectives.add(atRule)
+    }
+
     if (atRule.name === 'import') {
       if (atRule.params === '"tailwindcss/base"' || atRule.params === "'tailwindcss/base'") {
         atRule.name = 'tailwind'
@@ -74,5 +79,5 @@ export default function normalizeTailwindDirectives(root) {
     }
   }
 
-  return tailwindDirectives
+  return { tailwindDirectives, applyDirectives }
 }
diff --git a/src/lib/setupTrackingContext.js b/src/lib/setupTrackingContext.js
index d4015c5bf59e..49050fd3bdca 100644
--- a/src/lib/setupTrackingContext.js
+++ b/src/lib/setupTrackingContext.js
@@ -112,19 +112,20 @@ function resolveChangedFiles(candidateFiles, fileModifiedMap) {
 // source path), or set up a new one (including setting up watchers and registering
 // plugins) then return it
 export default function setupTrackingContext(configOrPath) {
-  return ({ tailwindDirectives, registerDependency }) => {
+  return ({ tailwindDirectives, registerDependency, applyDirectives }) => {
     return (root, result) => {
       let [tailwindConfig, userConfigPath, tailwindConfigHash, configDependencies] =
         getTailwindConfig(configOrPath)
 
       let contextDependencies = new Set(configDependencies)
 
-      // If there are no @tailwind rules, we don't consider this CSS file or it's dependencies
-      // to be dependencies of the context. Can reuse the context even if they change.
-      // We may want to think about `@layer` being part of this trigger too, but it's tough
-      // because it's impossible for a layer in one file to end up in the actual @tailwind rule
-      // in another file since independent sources are effectively isolated.
-      if (tailwindDirectives.size > 0) {
+      // If there are no @tailwind or @apply rules, we don't consider this CSS
+      // file or its dependencies to be dependencies of the context. Can reuse
+      // the context even if they change. We may want to think about `@layer`
+      // being part of this trigger too, but it's tough because it's impossible
+      // for a layer in one file to end up in the actual @tailwind rule in
+      // another file since independent sources are effectively isolated.
+      if (tailwindDirectives.size > 0 || applyDirectives.size > 0) {
         // Add current css file as a context dependencies.
         contextDependencies.add(result.opts.from)
 
@@ -147,12 +148,12 @@ export default function setupTrackingContext(configOrPath) {
 
       let candidateFiles = getCandidateFiles(context, tailwindConfig)
 
-      // If there are no @tailwind rules, we don't consider this CSS file or it's dependencies
-      // to be dependencies of the context. Can reuse the context even if they change.
+      // If there are no @tailwind or @apply rules, we don't consider this CSS file or it's
+      // dependencies to be dependencies of the context. Can reuse the context even if they change.
       // We may want to think about `@layer` being part of this trigger too, but it's tough
       // because it's impossible for a layer in one file to end up in the actual @tailwind rule
       // in another file since independent sources are effectively isolated.
-      if (tailwindDirectives.size > 0) {
+      if (tailwindDirectives.size > 0 || applyDirectives.size > 0) {
         let fileModifiedMap = getFileModifiedMap(context)
 
         // Add template paths as postcss dependencies.
diff --git a/src/processTailwindFeatures.js b/src/processTailwindFeatures.js
index 8a6d22dae744..7c622205b623 100644
--- a/src/processTailwindFeatures.js
+++ b/src/processTailwindFeatures.js
@@ -12,10 +12,11 @@ import { issueFlagNotices } from './featureFlags'
 
 export default function processTailwindFeatures(setupContext) {
   return function (root, result) {
-    let tailwindDirectives = normalizeTailwindDirectives(root)
+    let { tailwindDirectives, applyDirectives } = normalizeTailwindDirectives(root)
 
     let context = setupContext({
       tailwindDirectives,
+      applyDirectives,
       registerDependency(dependency) {
         result.messages.push({
           plugin: 'tailwindcss',
diff --git a/tests/apply.test.js b/tests/apply.test.js
index 59807a633129..25ca0b24cc5f 100644
--- a/tests/apply.test.js
+++ b/tests/apply.test.js
@@ -775,3 +775,38 @@ it('should not apply unrelated siblings when applying something from within atru
     `)
   })
 })
+
+it('should be possible to apply user css without tailwind directives', () => {
+  let config = {
+    content: [{ raw: html`<div class="foo"></div>` }],
+    plugins: [],
+  }
+
+  let input = css`
+    .bop {
+      color: red;
+    }
+    .bar {
+      background-color: blue;
+    }
+    .foo {
+      @apply absolute bar bop;
+    }
+  `
+
+  return run(input, config).then((result) => {
+    return expect(result.css).toMatchFormattedCss(css`
+      .bop {
+        color: red;
+      }
+      .bar {
+        background-color: blue;
+      }
+      .foo {
+        position: absolute;
+        color: red;
+        background-color: blue;
+      }
+    `)
+  })
+})