diff --git a/.changeset/recursive-filter-root-exclusion.md b/.changeset/recursive-filter-root-exclusion.md
new file mode 100644
index 0000000000..a4af404d96
--- /dev/null
+++ b/.changeset/recursive-filter-root-exclusion.md
@@ -0,0 +1,5 @@
+---
+"pnpm": patch
+---
+
+Fix a regression where `pnpm --recursive --filter '!<pkg>' run/exec/test/add` would include the workspace root in the matched projects. The workspace root is now correctly excluded by default when only negative `--filter` arguments are provided, matching the [documented behavior](https://pnpm.io/cli/recursive). To include the root, pass `--include-workspace-root` [#11341](https://github.com/pnpm/pnpm/issues/11341).
diff --git a/pnpm/src/main.ts b/pnpm/src/main.ts
index 2337a4dfd2..02457fc2e5 100644
--- a/pnpm/src/main.ts
+++ b/pnpm/src/main.ts
@@ -249,7 +249,7 @@ export async function main (inputArgv: string[]): Promise<void> {
     if (config.workspaceRoot) {
       filters.push({ filter: `{${relativeWSDirPath()}}`, followProdDepsOnly: Boolean(config.filterProd.length) })
     } else if (
-      filters.length === 0 &&
+      !filters.some(({ filter }) => !filter.startsWith('!')) &&
       workspaceDir &&
       config.workspacePackagePatterns &&
       !isRootOnlyPatterns(config.workspacePackagePatterns) &&
diff --git a/pnpm/test/recursive/filter.ts b/pnpm/test/recursive/filter.ts
index 881025f9e3..3470c76f82 100644
--- a/pnpm/test/recursive/filter.ts
+++ b/pnpm/test/recursive/filter.ts
@@ -1,7 +1,7 @@
 import fs from 'node:fs'
 
 import { expect, test } from '@jest/globals'
-import { prepare } from '@pnpm/prepare'
+import { prepare, preparePackages } from '@pnpm/prepare'
 
 import { execPnpmSync } from '../utils/index.js'
 
@@ -42,3 +42,115 @@ test('pnpm --filter . add <pkg> should work', async () => {
   const pkg = JSON.parse(fs.readFileSync('package.json', 'utf8'))
   expect(pkg.dependencies['is-positive']).toBeTruthy()
 })
+
+// Regression test for https://github.com/pnpm/pnpm/issues/11341
+test('pnpm --recursive --filter "!<pkg>" run should still exclude the workspace root', async () => {
+  preparePackages([
+    {
+      location: '.',
+      package: {
+        name: 'root',
+        version: '0.0.0',
+        private: true,
+        scripts: {
+          which: "node -e \"console.log('root')\"",
+        },
+      },
+    },
+    {
+      location: 'a',
+      package: {
+        name: 'a',
+        version: '1.0.0',
+        scripts: {
+          which: "node -e \"console.log('a')\"",
+        },
+      },
+    },
+    {
+      location: 'b',
+      package: {
+        name: 'b',
+        version: '1.0.0',
+        scripts: {
+          which: "node -e \"console.log('b')\"",
+        },
+      },
+    },
+  ])
+
+  fs.writeFileSync('pnpm-workspace.yaml', 'packages:\n  - "*"\n')
+
+  const result = execPnpmSync([
+    '--stream',
+    '--config.verify-deps-before-run=false',
+    '--recursive',
+    '--filter',
+    '!a',
+    'run',
+    'which',
+  ])
+  expect(result.status).toBe(0)
+
+  const stdout = result.stdout.toString()
+  expect(stdout).toContain('b which$')
+  // The `--stream` reporter prefixes lines with the project's relative directory,
+  // so the workspace root (cwd === wsDir) would appear as `. which$` if included.
+  expect(stdout).not.toContain('. which$')
+  expect(stdout).not.toContain('a which$')
+})
+
+test('pnpm --recursive --filter "!<pkg>" --include-workspace-root run should include the workspace root', async () => {
+  preparePackages([
+    {
+      location: '.',
+      package: {
+        name: 'root',
+        version: '0.0.0',
+        private: true,
+        scripts: {
+          which: "node -e \"console.log('root')\"",
+        },
+      },
+    },
+    {
+      location: 'a',
+      package: {
+        name: 'a',
+        version: '1.0.0',
+        scripts: {
+          which: "node -e \"console.log('a')\"",
+        },
+      },
+    },
+    {
+      location: 'b',
+      package: {
+        name: 'b',
+        version: '1.0.0',
+        scripts: {
+          which: "node -e \"console.log('b')\"",
+        },
+      },
+    },
+  ])
+
+  fs.writeFileSync('pnpm-workspace.yaml', 'packages:\n  - "*"\n')
+
+  const result = execPnpmSync([
+    '--stream',
+    '--config.verify-deps-before-run=false',
+    '--recursive',
+    '--include-workspace-root',
+    '--filter',
+    '!a',
+    'run',
+    'which',
+  ])
+  expect(result.status).toBe(0)
+
+  const stdout = result.stdout.toString()
+  expect(stdout).toContain('b which$')
+  expect(stdout).toContain('. which$')
+  expect(stdout).not.toContain('a which$')
+})