diff --git a/packages/shadcn/src/utils/dry-run-formatter.ts b/packages/shadcn/src/utils/dry-run-formatter.ts
index bd6b2bb3cb..d30cfbf33f 100644
--- a/packages/shadcn/src/utils/dry-run-formatter.ts
+++ b/packages/shadcn/src/utils/dry-run-formatter.ts
@@ -134,9 +134,7 @@ function formatSummaryOutput(result: DryRunResult, componentNames: string[]) {
 
   // Footer.
   lines.push(`${dim("│")} ${dim("Run with --diff to view changes.")}`)
-  lines.push(
-    `${dim("│")} ${dim("Run with --view to view file contents.")}`
-  )
+  lines.push(`${dim("│")} ${dim("Run with --view to view file contents.")}`)
   lines.push(`${dim("└")} ${dim("Run without --dry-run to apply.")}`)
 
   return lines.join("\n")
diff --git a/packages/shadcn/src/utils/updaters/update-css.ts b/packages/shadcn/src/utils/updaters/update-css.ts
index eb9b46cdf2..1727ff9ceb 100644
--- a/packages/shadcn/src/utils/updaters/update-css.ts
+++ b/packages/shadcn/src/utils/updaters/update-css.ts
@@ -15,6 +15,7 @@ import AtRule from "postcss/lib/at-rule"
 import Declaration from "postcss/lib/declaration"
 import Root from "postcss/lib/root"
 import Rule from "postcss/lib/rule"
+import { twMerge } from "tailwind-merge"
 import { z } from "zod"
 
 export async function updateCss(
@@ -564,13 +565,10 @@ function processRule(parent: Root | AtRule, selector: string, properties: any) {
                   node.type === "atrule" && node.name === "apply"
               )
               if (existingApply) {
-                const existingClasses = new Set(
-                  existingApply.params.split(/\s+/)
+                existingApply.params = twMerge(
+                  existingApply.params,
+                  atRuleParams
                 )
-                for (const cls of atRuleParams.split(/\s+/)) {
-                  existingClasses.add(cls)
-                }
-                existingApply.params = [...existingClasses].join(" ")
                 continue
               }
             }
diff --git a/packages/shadcn/test/utils/updaters/update-css.test.ts b/packages/shadcn/test/utils/updaters/update-css.test.ts
index e168f0dfeb..bd582569bc 100644
--- a/packages/shadcn/test/utils/updaters/update-css.test.ts
+++ b/packages/shadcn/test/utils/updaters/update-css.test.ts
@@ -1037,6 +1037,90 @@ describe("transformCss", () => {
     `)
   })
 
+  test("should merge @apply directives in the same rule instead of duplicating", async () => {
+    const input = `@import "tailwindcss";
+
+@layer base {
+  body {
+    @apply bg-background text-foreground;
+  }
+}`
+
+    const result = await transformCss(input, {
+      "@layer base": {
+        body: {
+          "@apply font-sans": {},
+        },
+      },
+    })
+
+    expect(result).toMatchInlineSnapshot(`
+      "@import "tailwindcss";
+
+      @layer base {
+        body {
+          @apply bg-background text-foreground font-sans;
+        }
+      }"
+    `)
+  })
+
+  test("should resolve conflicting tailwind classes when merging @apply", async () => {
+    const input = `@import "tailwindcss";
+
+@layer base {
+  body {
+    @apply bg-background font-serif text-foreground;
+  }
+}`
+
+    const result = await transformCss(input, {
+      "@layer base": {
+        body: {
+          "@apply font-mono": {},
+        },
+      },
+    })
+
+    expect(result).toMatchInlineSnapshot(`
+      "@import "tailwindcss";
+
+      @layer base {
+        body {
+          @apply bg-background text-foreground font-mono;
+        }
+      }"
+    `)
+  })
+
+  test("should not duplicate @apply classes that already exist", async () => {
+    const input = `@import "tailwindcss";
+
+@layer base {
+  body {
+    @apply bg-background text-foreground font-sans;
+  }
+}`
+
+    const result = await transformCss(input, {
+      "@layer base": {
+        body: {
+          "@apply font-sans": {},
+        },
+      },
+    })
+
+    expect(result).toMatchInlineSnapshot(`
+      "@import "tailwindcss";
+
+      @layer base {
+        body {
+          @apply bg-background text-foreground font-sans;
+        }
+      }"
+    `)
+  })
+
   test("should replace existing keyframes instead of duplicating", async () => {
     const input = `@import "tailwindcss";