diff --git a/.changeset/fix-recursive-run-no-script.md b/.changeset/fix-recursive-run-no-script.md
new file mode 100644
index 0000000000..db71460db8
--- /dev/null
+++ b/.changeset/fix-recursive-run-no-script.md
@@ -0,0 +1,6 @@
+---
+"pnpm": patch
+"@pnpm/plugin-commands-script-runners": patch
+---
+
+`pnpm run -r` and `pnpm run --filter` now fail with a non-zero exit code when no packages have the specified script. Previously, this only failed when all packages were selected. Use `--if-present` to suppress this error [#6844](https://github.com/pnpm/pnpm/issues/6844).
diff --git a/exec/plugin-commands-script-runners/src/runRecursive.ts b/exec/plugin-commands-script-runners/src/runRecursive.ts
index 2a64011cca..7de1c91cb4 100644
--- a/exec/plugin-commands-script-runners/src/runRecursive.ts
+++ b/exec/plugin-commands-script-runners/src/runRecursive.ts
@@ -8,7 +8,6 @@ import {
   makeNodeRequireOption,
   type RunLifecycleHookOptions,
 } from '@pnpm/lifecycle'
-import { logger } from '@pnpm/logger'
 import { groupStart } from '@pnpm/log.group'
 import { sortPackages } from '@pnpm/sort-packages'
 import pLimit from 'p-limit'
@@ -187,10 +186,7 @@ export async function runRecursive (
     if (allPackagesAreSelected) {
       throw new PnpmError('RECURSIVE_RUN_NO_SCRIPT', `None of the packages has a "${scriptName}" script`)
     } else {
-      logger.info({
-        message: `None of the selected packages has a "${scriptName}" script`,
-        prefix: opts.workspaceDir,
-      })
+      throw new PnpmError('RECURSIVE_RUN_NO_SCRIPT', `None of the selected packages has a "${scriptName}" script`)
     }
   }
   opts.reportSummary && await writeRecursiveSummary({
diff --git a/exec/plugin-commands-script-runners/test/runRecursive.ts b/exec/plugin-commands-script-runners/test/runRecursive.ts
index 8b9ac8c5ed..c57ec1fabf 100644
--- a/exec/plugin-commands-script-runners/test/runRecursive.ts
+++ b/exec/plugin-commands-script-runners/test/runRecursive.ts
@@ -380,7 +380,7 @@ test('`pnpm recursive run` fails when run with a filter that includes all packag
   expect(err.code).toBe('ERR_PNPM_RECURSIVE_RUN_NO_SCRIPT')
 })
 
-test('`pnpm recursive run` succeeds when run against a subset of packages and no package has the desired command', async () => {
+test('`pnpm recursive run` fails when run against a subset of packages and no package has the desired command, unless if-present is set', async () => {
   preparePackages([
     {
       name: 'project-1',
@@ -422,14 +422,28 @@ test('`pnpm recursive run` succeeds when run against a subset of packages and no
     [{ namePattern: 'project-1' }],
     { workspaceDir: process.cwd() }
   )
+
+  // Recursive run does not fail when if-present is true
   await run.handler({
     ...DEFAULT_OPTS,
     allProjects,
     dir: process.cwd(),
+    ifPresent: true,
     recursive: true,
     selectedProjectsGraph,
     workspaceDir: process.cwd(),
   }, ['this-command-does-not-exist'])
+
+  await expect(
+    run.handler({
+      ...DEFAULT_OPTS,
+      allProjects,
+      dir: process.cwd(),
+      recursive: true,
+      selectedProjectsGraph,
+      workspaceDir: process.cwd(),
+    }, ['this-command-does-not-exist'])
+  ).rejects.toThrow(/None of the selected packages has a/)
 })
 
 test('"pnpm run --filter <pkg>" without specifying the script name', async () => {