diff --git a/.changeset/grumpy-moles-ring.md b/.changeset/grumpy-moles-ring.md
new file mode 100644
index 0000000000..fb5e280e14
--- /dev/null
+++ b/.changeset/grumpy-moles-ring.md
@@ -0,0 +1,5 @@
+---
+"shadcn": patch
+---
+
+update template handling
diff --git a/.github/workflows/templates.yml b/.github/workflows/templates.yml
index d22cccf2d7..f50a6127cc 100644
--- a/.github/workflows/templates.yml
+++ b/.github/workflows/templates.yml
@@ -131,6 +131,7 @@ jobs:
             local package_manager="$1"
             local project_path="$2"
             local check_workspace_protocol="$3"
+            local is_monorepo="$4"
 
             cd "$project_path"
             test ! -f pnpm-workspace.yaml
@@ -138,6 +139,7 @@ jobs:
 
             EXPECTED_PACKAGE_MANAGER="$package_manager" \
               CHECK_WORKSPACE_PROTOCOL="$check_workspace_protocol" \
+              IS_MONOREPO="$is_monorepo" \
               node <<'NODE'
           const fs = require("node:fs")
           const path = require("node:path")
@@ -145,27 +147,41 @@ jobs:
           const expectedPackageManager = process.env.EXPECTED_PACKAGE_MANAGER
           const checkWorkspaceProtocol =
             process.env.CHECK_WORKSPACE_PROTOCOL === "true"
+          const isMonorepo = process.env.IS_MONOREPO === "true"
           const pkg = JSON.parse(fs.readFileSync("package.json", "utf8"))
-          const workspaces = pkg.workspaces ?? []
 
-          if (!Array.isArray(workspaces)) {
-            throw new Error("Expected package.json workspaces to be an array.")
-          }
+          if (isMonorepo) {
+            const workspaces = pkg.workspaces ?? []
 
-          if (workspaces.length === 0) {
-            throw new Error("Expected package.json workspaces to have entries.")
-          }
-
-          for (const workspace of ["sharp", "unrs-resolver", "esbuild"]) {
-            if (workspaces.includes(workspace)) {
-              throw new Error(`Unexpected workspace entry: ${workspace}`)
+            if (!Array.isArray(workspaces)) {
+              throw new Error("Expected package.json workspaces to be an array.")
             }
-          }
 
-          if (!pkg.packageManager?.startsWith(`${expectedPackageManager}@`)) {
-            throw new Error(
-              `Expected packageManager to use ${expectedPackageManager}, got ${pkg.packageManager}`
-            )
+            if (workspaces.length === 0) {
+              throw new Error("Expected package.json workspaces to have entries.")
+            }
+
+            for (const workspace of ["sharp", "unrs-resolver", "esbuild"]) {
+              if (workspaces.includes(workspace)) {
+                throw new Error(`Unexpected workspace entry: ${workspace}`)
+              }
+            }
+
+            if (!pkg.packageManager?.startsWith(`${expectedPackageManager}@`)) {
+              throw new Error(
+                `Expected packageManager to use ${expectedPackageManager}, got ${pkg.packageManager}`
+              )
+            }
+          } else {
+            if (pkg.workspaces !== undefined) {
+              throw new Error("Did not expect package.json workspaces for app template.")
+            }
+
+            if (pkg.packageManager !== undefined) {
+              throw new Error(
+                `Did not expect packageManager for app template, got ${pkg.packageManager}`
+              )
+            }
           }
 
           if (checkWorkspaceProtocol) {
@@ -213,8 +229,10 @@ jobs:
 
             if [ "$mode" = "monorepo" ]; then
               args+=(--monorepo)
+              is_monorepo="true"
             else
               args+=(--no-monorepo)
+              is_monorepo="false"
             fi
 
             case "$TEMPLATE_PACKAGE_MANAGER" in
@@ -238,7 +256,11 @@ jobs:
                     bunx --bun --package "$GITHUB_WORKSPACE/packages/shadcn" \
                       shadcn "${args[@]}"
                 )
-                validate_non_pnpm_project "bun" "$project_path" "false"
+                validate_non_pnpm_project \
+                  "bun" \
+                  "$project_path" \
+                  "false" \
+                  "$is_monorepo"
                 ;;
               npm)
                 (
@@ -249,7 +271,11 @@ jobs:
                     npx --yes --package "$GITHUB_WORKSPACE/packages/shadcn" \
                       shadcn "${args[@]}"
                 )
-                validate_non_pnpm_project "npm" "$project_path" "true"
+                validate_non_pnpm_project \
+                  "npm" \
+                  "$project_path" \
+                  "true" \
+                  "$is_monorepo"
                 ;;
               yarn)
                 (
@@ -261,7 +287,11 @@ jobs:
                     yarn dlx --package "$GITHUB_WORKSPACE/packages/shadcn" \
                       shadcn "${args[@]}"
                 )
-                validate_non_pnpm_project "yarn" "$project_path" "false"
+                validate_non_pnpm_project \
+                  "yarn" \
+                  "$project_path" \
+                  "false" \
+                  "$is_monorepo"
                 ;;
             esac
 
diff --git a/packages/shadcn/src/templates/create-template.ts b/packages/shadcn/src/templates/create-template.ts
index 35b071ab7c..c1a5376d69 100644
--- a/packages/shadcn/src/templates/create-template.ts
+++ b/packages/shadcn/src/templates/create-template.ts
@@ -127,7 +127,11 @@ async function adaptWorkspaceConfig(
     await fs.remove(lockFilePath)
   }
 
-  const isMonorepo = fs.existsSync(pnpmWorkspacePath)
+  const hasPnpmWorkspaceConfig = fs.existsSync(pnpmWorkspacePath)
+  const workspacePatterns = hasPnpmWorkspaceConfig
+    ? parsePnpmWorkspacePackages(await fs.readFile(pnpmWorkspacePath, "utf8"))
+    : []
+  const isMonorepo = workspacePatterns.length > 0
 
   // Update root package.json: update "packageManager" field for the
   // target package manager, and add "workspaces" for npm/bun/yarn.
@@ -145,12 +149,7 @@ async function adaptWorkspaceConfig(
     }
 
     if (isMonorepo) {
-      // Read workspace patterns from pnpm-workspace.yaml.
-      const workspaceContent = await fs.readFile(pnpmWorkspacePath, "utf8")
-      const patterns = parsePnpmWorkspacePackages(workspaceContent)
-
-      packageJson.workspaces = patterns
-      await fs.remove(pnpmWorkspacePath)
+      packageJson.workspaces = workspacePatterns
     }
 
     await fs.writeFile(
@@ -159,6 +158,10 @@ async function adaptWorkspaceConfig(
     )
   }
 
+  if (hasPnpmWorkspaceConfig) {
+    await fs.remove(pnpmWorkspacePath)
+  }
+
   // Rewrite workspace: protocol references in nested package.json files.
   // npm does not support workspace: protocol; bun and yarn do, so only
   // rewrite for npm monorepo templates.
diff --git a/packages/shadcn/src/utils/scaffold.test.ts b/packages/shadcn/src/utils/scaffold.test.ts
index d0b3e01be3..35a6157eae 100644
--- a/packages/shadcn/src/utils/scaffold.test.ts
+++ b/packages/shadcn/src/utils/scaffold.test.ts
@@ -338,6 +338,84 @@ describe("defaultScaffold", () => {
     expect(written.packageManager).toBe("bun@1.2.0")
   })
 
+  it("should remove pnpm-only workspace config for non-pnpm templates", async () => {
+    vi.mocked(fs.existsSync).mockImplementation((p: any) => {
+      const s = p.toString()
+      return s.includes("pnpm-workspace.yaml") || s.includes("package.json")
+    })
+
+    vi.mocked(fs.readFile).mockImplementation(((filePath: string) => {
+      if (filePath.includes("pnpm-workspace.yaml")) {
+        return Promise.resolve("allowBuilds:\n  esbuild: true\n")
+      }
+      return Promise.resolve(
+        JSON.stringify({ name: "my-app", packageManager: "pnpm@9.0.0" })
+      )
+    }) as any)
+
+    const template = createTestTemplate()
+
+    await template.scaffold({
+      projectPath: "/test/my-app",
+      packageManager: "bun",
+      cwd: "/test",
+    })
+
+    expect(vi.mocked(fs.remove)).toHaveBeenCalledWith(
+      path.join("/test/my-app", "pnpm-workspace.yaml")
+    )
+
+    const writeCalls = vi.mocked(fs.writeFile).mock.calls
+    const adaptCall = writeCalls.find(
+      (call) => call[0] === path.join("/test/my-app", "package.json")
+    )
+    expect(adaptCall).toBeDefined()
+    const written = JSON.parse(adaptCall![1] as string)
+    expect(written.packageManager).toBeUndefined()
+    expect(written.workspaces).toBeUndefined()
+  })
+
+  it("should treat single-app workspace yaml (packages:[] + allowBuilds) as non-monorepo", async () => {
+    vi.mocked(fs.existsSync).mockImplementation((p: any) => {
+      const s = p.toString()
+      return s.includes("pnpm-workspace.yaml") || s.includes("package.json")
+    })
+
+    vi.mocked(fs.readFile).mockImplementation(((filePath: string) => {
+      if (filePath.includes("pnpm-workspace.yaml")) {
+        return Promise.resolve(
+          "packages: []\n\nallowBuilds:\n  esbuild: true\n"
+        )
+      }
+      return Promise.resolve(
+        JSON.stringify({ name: "my-app", packageManager: "pnpm@9.0.0" })
+      )
+    }) as any)
+
+    const template = createTestTemplate()
+
+    await template.scaffold({
+      projectPath: "/test/my-app",
+      packageManager: "npm",
+      cwd: "/test",
+    })
+
+    // Inline empty packages array must not be parsed as a monorepo;
+    // the yaml is stripped and no workspaces array is added.
+    expect(vi.mocked(fs.remove)).toHaveBeenCalledWith(
+      path.join("/test/my-app", "pnpm-workspace.yaml")
+    )
+
+    const writeCalls = vi.mocked(fs.writeFile).mock.calls
+    const adaptCall = writeCalls.find(
+      (call) => call[0] === path.join("/test/my-app", "package.json")
+    )
+    expect(adaptCall).toBeDefined()
+    const written = JSON.parse(adaptCall![1] as string)
+    expect(written.packageManager).toBeUndefined()
+    expect(written.workspaces).toBeUndefined()
+  })
+
   it("should rewrite workspace: protocol refs to * for npm monorepo", async () => {
     vi.mocked(fs.existsSync).mockImplementation((p: any) => {
       const s = p.toString()
diff --git a/templates/astro-app/pnpm-workspace.yaml b/templates/astro-app/pnpm-workspace.yaml
index 30da592674..96142df1cf 100644
--- a/templates/astro-app/pnpm-workspace.yaml
+++ b/templates/astro-app/pnpm-workspace.yaml
@@ -1,5 +1,6 @@
-packages:
-  - "."
+packages: []
 
-ignoredBuiltDependencies:
-  - esbuild
+allowBuilds:
+  esbuild: true
+  sharp: true
+  msw: false
diff --git a/templates/astro-monorepo/pnpm-workspace.yaml b/templates/astro-monorepo/pnpm-workspace.yaml
index f7e31c2a92..0868ac4a58 100644
--- a/templates/astro-monorepo/pnpm-workspace.yaml
+++ b/templates/astro-monorepo/pnpm-workspace.yaml
@@ -2,6 +2,7 @@ packages:
   - "apps/*"
   - "packages/*"
 
-ignoredBuiltDependencies:
-  - esbuild
-
+allowBuilds:
+  esbuild: true
+  sharp: true
+  msw: false
diff --git a/templates/next-app/pnpm-workspace.yaml b/templates/next-app/pnpm-workspace.yaml
index cc26c4c27d..b71df62daf 100644
--- a/templates/next-app/pnpm-workspace.yaml
+++ b/templates/next-app/pnpm-workspace.yaml
@@ -1,6 +1,6 @@
-packages:
-  - "."
+packages: []
 
-ignoredBuiltDependencies:
-  - sharp
-  - unrs-resolver
+allowBuilds:
+  sharp: true
+  unrs-resolver: true
+  msw: false
diff --git a/templates/next-monorepo/pnpm-workspace.yaml b/templates/next-monorepo/pnpm-workspace.yaml
index d54bfbfc65..7d14a584fe 100644
--- a/templates/next-monorepo/pnpm-workspace.yaml
+++ b/templates/next-monorepo/pnpm-workspace.yaml
@@ -2,7 +2,7 @@ packages:
   - "apps/*"
   - "packages/*"
 
-ignoredBuiltDependencies:
-  - sharp
-  - unrs-resolver
-
+allowBuilds:
+  sharp: true
+  unrs-resolver: true
+  msw: false
diff --git a/templates/react-router-app/pnpm-workspace.yaml b/templates/react-router-app/pnpm-workspace.yaml
index 30da592674..6afd1d41d7 100644
--- a/templates/react-router-app/pnpm-workspace.yaml
+++ b/templates/react-router-app/pnpm-workspace.yaml
@@ -1,5 +1,5 @@
-packages:
-  - "."
+packages: []
 
-ignoredBuiltDependencies:
-  - esbuild
+allowBuilds:
+  esbuild: true
+  msw: false
diff --git a/templates/react-router-monorepo/pnpm-workspace.yaml b/templates/react-router-monorepo/pnpm-workspace.yaml
index f7e31c2a92..f4b5328698 100644
--- a/templates/react-router-monorepo/pnpm-workspace.yaml
+++ b/templates/react-router-monorepo/pnpm-workspace.yaml
@@ -2,6 +2,6 @@ packages:
   - "apps/*"
   - "packages/*"
 
-ignoredBuiltDependencies:
-  - esbuild
-
+allowBuilds:
+  esbuild: true
+  msw: false
diff --git a/templates/start-app/pnpm-workspace.yaml b/templates/start-app/pnpm-workspace.yaml
index 67a9414e0f..ba438ef7cf 100644
--- a/templates/start-app/pnpm-workspace.yaml
+++ b/templates/start-app/pnpm-workspace.yaml
@@ -1,6 +1,7 @@
-packages:
-  - "."
+packages: []
 
-onlyBuiltDependencies:
-  - esbuild
-  - lightningcss
+allowBuilds:
+  esbuild: true
+  lightningcss: true
+  unrs-resolver: true
+  msw: false
diff --git a/templates/start-monorepo/pnpm-workspace.yaml b/templates/start-monorepo/pnpm-workspace.yaml
index 3ff5faaaf5..926cd294cb 100644
--- a/templates/start-monorepo/pnpm-workspace.yaml
+++ b/templates/start-monorepo/pnpm-workspace.yaml
@@ -1,3 +1,9 @@
 packages:
   - "apps/*"
   - "packages/*"
+
+allowBuilds:
+  esbuild: true
+  lightningcss: true
+  unrs-resolver: true
+  msw: false
diff --git a/templates/vite-app/pnpm-workspace.yaml b/templates/vite-app/pnpm-workspace.yaml
index 30da592674..6afd1d41d7 100644
--- a/templates/vite-app/pnpm-workspace.yaml
+++ b/templates/vite-app/pnpm-workspace.yaml
@@ -1,5 +1,5 @@
-packages:
-  - "."
+packages: []
 
-ignoredBuiltDependencies:
-  - esbuild
+allowBuilds:
+  esbuild: true
+  msw: false
diff --git a/templates/vite-monorepo/pnpm-workspace.yaml b/templates/vite-monorepo/pnpm-workspace.yaml
index f7e31c2a92..f4b5328698 100644
--- a/templates/vite-monorepo/pnpm-workspace.yaml
+++ b/templates/vite-monorepo/pnpm-workspace.yaml
@@ -2,6 +2,6 @@ packages:
   - "apps/*"
   - "packages/*"
 
-ignoredBuiltDependencies:
-  - esbuild
-
+allowBuilds:
+  esbuild: true
+  msw: false