diff --git a/src/lib/expandApplyAtRules.js b/src/lib/expandApplyAtRules.js
index cdcd0b5688c9..836e9ba86c22 100644
--- a/src/lib/expandApplyAtRules.js
+++ b/src/lib/expandApplyAtRules.js
@@ -4,6 +4,7 @@ import parser from 'postcss-selector-parser'
 import { resolveMatches } from './generateRules'
 import escapeClassName from '../util/escapeClassName'
 import { applyImportantSelector } from '../util/applyImportantSelector'
+import { collectPseudoElements, sortSelector } from '../util/formatVariantSelector.js'
 
 /** @typedef {Map<string, [any, import('postcss').Rule[]]>} ApplyCache */
 
@@ -562,6 +563,17 @@ function processApply(root, context, localCache) {
             rule.walkDecls((d) => {
               d.important = meta.important || important
             })
+
+            // Move pseudo elements to the end of the selector (if necessary)
+            let selector = parser().astSync(rule.selector)
+            selector.each((sel) => {
+              let [pseudoElements] = collectPseudoElements(sel, true, [':is', ':has'])
+              if (pseudoElements.length > 0) {
+                sel.nodes.push(...pseudoElements.sort(sortSelector))
+              }
+            })
+
+            rule.selector = selector.toString()
           })
         }
 
diff --git a/src/util/formatVariantSelector.js b/src/util/formatVariantSelector.js
index da5e2c78dfbc..062437061f9d 100644
--- a/src/util/formatVariantSelector.js
+++ b/src/util/formatVariantSelector.js
@@ -246,7 +246,7 @@ export function finalizeSelector(current, formats, { context, candidate, base })
 
   // Move pseudo elements to the end of the selector (if necessary)
   selector.each((sel) => {
-    let pseudoElements = collectPseudoElements(sel)
+    let [pseudoElements] = collectPseudoElements(sel)
     if (pseudoElements.length > 0) {
       sel.nodes.push(pseudoElements.sort(sortSelector))
     }
@@ -339,6 +339,17 @@ let pseudoElementExceptions = [
   '::-webkit-resizer',
 ]
 
+export function containsNode(selector, values) {
+  let found = false
+  selector.walk((node) => {
+    if (values.includes(node.value)) {
+      found = true
+      return false
+    }
+  })
+  return found
+}
+
 /**
  * This will make sure to move pseudo's to the correct spot (the end for
  * pseudo elements) because otherwise the selector will never work
@@ -351,23 +362,43 @@ let pseudoElementExceptions = [
  * `::before:hover` doesn't work, which means that we can make it work for you by flipping the order.
  *
  * @param {Selector} selector
+ * @param {boolean} force
+ * @param {string[]|null} safelist
  **/
-function collectPseudoElements(selector) {
+export function collectPseudoElements(selector, force = false, safelist = null) {
   /** @type {Node[]} */
   let nodes = []
+  let seenPseudoElement = null
+
+  if (safelist !== null && !containsNode(selector, safelist)) {
+    return [[], seenPseudoElement]
+  }
 
-  for (let node of selector.nodes) {
-    if (isPseudoElement(node)) {
+  for (let node of [...selector.nodes]) {
+    if (isPseudoElement(node, force)) {
       nodes.push(node)
       selector.removeChild(node)
+      seenPseudoElement = node.value
+    } else if (seenPseudoElement !== null) {
+      if (pseudoElementExceptions.includes(seenPseudoElement) && isPseudoClass(node, force)) {
+        nodes.push(node)
+        selector.removeChild(node)
+      } else {
+        seenPseudoElement = null
+      }
     }
 
     if (node?.nodes) {
-      nodes.push(...collectPseudoElements(node))
+      let [collected, seenPseudoElementInSelector] = collectPseudoElements(node, force)
+      if (seenPseudoElementInSelector) {
+        seenPseudoElement = seenPseudoElementInSelector
+      }
+
+      nodes.push(...collected)
     }
   }
 
-  return nodes
+  return [nodes, seenPseudoElement]
 }
 
 // This will make sure to move pseudo's to the correct spot (the end for
@@ -380,7 +411,7 @@ function collectPseudoElements(selector) {
 //
 // `::before:hover` doesn't work, which means that we can make it work
 // for you by flipping the order.
-function sortSelector(a, z) {
+export function sortSelector(a, z) {
   // Both nodes are non-pseudo's so we can safely ignore them and keep
   // them in the same order.
   if (a.type !== 'pseudo' && z.type !== 'pseudo') {
@@ -404,9 +435,13 @@ function sortSelector(a, z) {
   return isPseudoElement(a) - isPseudoElement(z)
 }
 
-function isPseudoElement(node) {
+function isPseudoElement(node, force = false) {
   if (node.type !== 'pseudo') return false
-  if (pseudoElementExceptions.includes(node.value)) return false
+  if (pseudoElementExceptions.includes(node.value) && !force) return false
 
   return node.value.startsWith('::') || pseudoElementsBC.includes(node.value)
 }
+
+function isPseudoClass(node, force) {
+  return node.type === 'pseudo' && !isPseudoElement(node, force)
+}
diff --git a/tests/apply.test.js b/tests/apply.test.js
index f7fab7d70938..0ab9ec17567f 100644
--- a/tests/apply.test.js
+++ b/tests/apply.test.js
@@ -2357,4 +2357,74 @@ crosscheck(({ stable, oxide }) => {
       `)
     })
   })
+
+  it('pseudo elements inside apply are moved outside of :is() or :has()', () => {
+    let config = {
+      darkMode: 'class',
+      content: [
+        {
+          raw: html` <div class="foo bar baz qux steve bob"></div> `,
+        },
+      ],
+    }
+
+    let input = css`
+      .foo::before {
+        @apply dark:bg-black/100;
+      }
+
+      .bar::before {
+        @apply rtl:dark:bg-black/100;
+      }
+
+      .baz::before {
+        @apply rtl:dark:hover:bg-black/100;
+      }
+
+      .qux::file-selector-button {
+        @apply rtl:dark:hover:bg-black/100;
+      }
+
+      .steve::before {
+        @apply rtl:hover:dark:bg-black/100;
+      }
+
+      .bob::file-selector-button {
+        @apply rtl:hover:dark:bg-black/100;
+      }
+
+      .foo::before {
+        @apply [:has([dir="rtl"]_&)]:hover:bg-black/100;
+      }
+
+      .bar::file-selector-button {
+        @apply [:has([dir="rtl"]_&)]:hover:bg-black/100;
+      }
+    `
+
+    return run(input, config).then((result) => {
+      expect(result.css).toMatchFormattedCss(css`
+        :is(.dark .foo)::before,
+        :is([dir='rtl'] :is(.dark .bar))::before,
+        :is([dir='rtl'] :is(.dark .baz:hover))::before {
+          background-color: #000;
+        }
+        :is([dir='rtl'] :is(.dark .qux))::file-selector-button:hover {
+          background-color: #000;
+        }
+        :is([dir='rtl'] :is(.dark .steve):hover):before {
+          background-color: #000;
+        }
+        :is([dir='rtl'] :is(.dark .bob))::file-selector-button:hover {
+          background-color: #000;
+        }
+        :has([dir='rtl'] .foo:hover):before {
+          background-color: #000;
+        }
+        :has([dir='rtl'] .bar)::file-selector-button:hover {
+          background-color: #000;
+        }
+      `)
+    })
+  })
 })