diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6f4a575b5..4a2aecbc2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Ensure opacity modifier with variables work with `color-mix()` ([#13972](https://github.com/tailwindlabs/tailwindcss/pull/13972))
 - Discard invalid `variants` and `utilities` with modifiers ([#13977](https://github.com/tailwindlabs/tailwindcss/pull/13977))
 - Add missing utilities that exist in v3, such as `resize`, `fill-none`, `accent-none`, `drop-shadow-none`, and negative `hue-rotate` and `backdrop-hue-rotate` utilities ([#13971](https://github.com/tailwindlabs/tailwindcss/pull/13971))
+- Don’t allow at-rule-only variants to be compounded ([#14015](https://github.com/tailwindlabs/tailwindcss/pull/14015))
 
 ### Added
 
diff --git a/packages/tailwindcss/src/variants.test.ts b/packages/tailwindcss/src/variants.test.ts
index 9c1021fb4..e22b0a953 100644
--- a/packages/tailwindcss/src/variants.test.ts
+++ b/packages/tailwindcss/src/variants.test.ts
@@ -725,6 +725,15 @@ test('group-[...]', () => {
       display: flex;
     }"
   `)
+
+  expect(
+    compileCss(
+      css`
+        @tailwind utilities;
+      `,
+      ['group-[@media_foo]:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('group-*', () => {
@@ -752,6 +761,16 @@ test('group-*', () => {
       display: flex;
     }"
   `)
+
+  expect(
+    compileCss(
+      css`
+        @variant custom-at-rule (@media foo);
+        @tailwind utilities;
+      `,
+      ['group-custom-at-rule:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('peer-[...]', () => {
@@ -784,6 +803,15 @@ test('peer-[...]', () => {
       display: flex;
     }"
   `)
+
+  expect(
+    compileCss(
+      css`
+        @tailwind utilities;
+      `,
+      ['peer-[@media_foo]:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('peer-*', () => {
@@ -811,6 +839,16 @@ test('peer-*', () => {
       display: flex;
     }"
   `)
+
+  expect(
+    compileCss(
+      css`
+        @variant custom-at-rule (@media foo);
+        @tailwind utilities;
+      `,
+      ['peer-custom-at-rule:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('ltr', () => {
@@ -1505,7 +1543,15 @@ test('not', () => {
     }"
   `)
 
-  expect(run(['not-[:checked]/foo:flex'])).toEqual('')
+  expect(
+    compileCss(
+      css`
+        @variant custom-at-rule (@media foo);
+        @tailwind utilities;
+      `,
+      ['not-[:checked]/foo:flex', 'not-[@media_print]:flex', 'not-custom-at-rule:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('has', () => {
@@ -1518,7 +1564,7 @@ test('has', () => {
       'group-has-checked:flex',
 
       'peer-has-[:checked]:flex',
-      'peer-has-[:checked]/parent-name:flex',
+      'peer-has-[:checked]/sibling-name:flex',
       'peer-has-checked:flex',
     ]),
   ).toMatchInlineSnapshot(`
@@ -1542,7 +1588,7 @@ test('has', () => {
       display: flex;
     }
 
-    .peer-has-\\[\\:checked\\]\\/parent-name\\:flex:is(:where(.peer\\/parent-name):has(:checked) ~ *) {
+    .peer-has-\\[\\:checked\\]\\/sibling-name\\:flex:is(:where(.peer\\/sibling-name):has(:checked) ~ *) {
       display: flex;
     }
 
@@ -1550,7 +1596,16 @@ test('has', () => {
       display: flex;
     }"
   `)
-  expect(run(['has-[:checked]/foo:flex'])).toEqual('')
+
+  expect(
+    compileCss(
+      css`
+        @variant custom-at-rule (@media foo);
+        @tailwind utilities;
+      `,
+      ['has-[:checked]/foo:flex', 'has-[@media_print]:flex', 'has-custom-at-rule:flex'],
+    ),
+  ).toEqual('')
 })
 
 test('aria', () => {
diff --git a/packages/tailwindcss/src/variants.ts b/packages/tailwindcss/src/variants.ts
index 5be68c489..c3c50bc63 100644
--- a/packages/tailwindcss/src/variants.ts
+++ b/packages/tailwindcss/src/variants.ts
@@ -205,7 +205,28 @@ export function createVariants(theme: Theme): Variants {
 
   variants.compound('not', (ruleNode, variant) => {
     if (variant.modifier) return null
-    ruleNode.selector = `&:not(${ruleNode.selector.replace('&', '*')})`
+
+    let didApply = false
+
+    walk([ruleNode], (node) => {
+      if (node.kind !== 'rule') return WalkAction.Continue
+
+      // Skip past at-rules, and continue traversing the children of the at-rule
+      if (node.selector[0] === '@') return WalkAction.Continue
+
+      // Replace `&` in target variant with `*`, so variants like `&:hover`
+      // become `&:not(*:hover)`. The `*` will often be optimized away.
+      node.selector = `&:not(${node.selector.replace('&', '*')})`
+
+      // Track that the variant was actually applied
+      didApply = true
+    })
+
+    // If the node wasn't modified, this variant is not compatible with
+    // `not-*` so discard the candidate.
+    if (!didApply) {
+      return null
+    }
   })
 
   variants.compound('group', (ruleNode, variant) => {
@@ -215,6 +236,8 @@ export function createVariants(theme: Theme): Variants {
       ? `:where(.group\\/${variant.modifier.value})`
       : ':where(.group)'
 
+    let didApply = false
+
     walk([ruleNode], (node) => {
       if (node.kind !== 'rule') return WalkAction.Continue
 
@@ -234,10 +257,17 @@ export function createVariants(theme: Theme): Variants {
         node.selector = `:is(${node.selector})`
       }
 
-      // Use `:where` to make sure the specificity of group variants isn't higher
-      // than the specificity of other variants.
       node.selector = `&:is(${node.selector} *)`
+
+      // Track that the variant was actually applied
+      didApply = true
     })
+
+    // If the node wasn't modified, this variant is not compatible with
+    // `group-*` so discard the candidate.
+    if (!didApply) {
+      return null
+    }
   })
 
   variants.suggest('group', () => {
@@ -253,6 +283,8 @@ export function createVariants(theme: Theme): Variants {
       ? `:where(.peer\\/${variant.modifier.value})`
       : ':where(.peer)'
 
+    let didApply = false
+
     walk([ruleNode], (node) => {
       if (node.kind !== 'rule') return WalkAction.Continue
 
@@ -272,10 +304,17 @@ export function createVariants(theme: Theme): Variants {
         node.selector = `:is(${node.selector})`
       }
 
-      // Use `:where` to make sure the specificity of group variants isn't higher
-      // than the specificity of other variants.
       node.selector = `&:is(${node.selector} ~ *)`
+
+      // Track that the variant was actually applied
+      didApply = true
     })
+
+    // If the node wasn't modified, this variant is not compatible with
+    // `peer-*` so discard the candidate.
+    if (!didApply) {
+      return null
+    }
   })
 
   variants.suggest('peer', () => {
@@ -392,7 +431,28 @@ export function createVariants(theme: Theme): Variants {
 
   variants.compound('has', (ruleNode, variant) => {
     if (variant.modifier) return null
-    ruleNode.selector = `&:has(${ruleNode.selector.replace('&', '*')})`
+
+    let didApply = false
+
+    walk([ruleNode], (node) => {
+      if (node.kind !== 'rule') return WalkAction.Continue
+
+      // Skip past at-rules, and continue traversing the children of the at-rule
+      if (node.selector[0] === '@') return WalkAction.Continue
+
+      // Replace `&` in target variant with `*`, so variants like `&:hover`
+      // become `&:has(*:hover)`. The `*` will often be optimized away.
+      node.selector = `&:has(${node.selector.replace('&', '*')})`
+
+      // Track that the variant was actually applied
+      didApply = true
+    })
+
+    // If the node wasn't modified, this variant is not compatible with
+    // `has-*` so discard the candidate.
+    if (!didApply) {
+      return null
+    }
   })
 
   variants.suggest('has', () => {