diff --git a/.changeset/runtime-set-workspace-root.md b/.changeset/runtime-set-workspace-root.md
new file mode 100644
index 0000000000..c066dc0cd2
--- /dev/null
+++ b/.changeset/runtime-set-workspace-root.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/engine.runtime.commands": patch
+"pnpm": patch
+---
+
+`pnpm runtime set <name> <version>` no longer fails in the root of a multi-package workspace with the `ADDING_TO_ROOT` error. Installing the workspace root is a valid target for a runtime, so the command now bypasses that safety check.
diff --git a/engine/runtime/commands/src/runtime/runtime.ts b/engine/runtime/commands/src/runtime/runtime.ts
index 9c769a7a20..49ac563434 100644
--- a/engine/runtime/commands/src/runtime/runtime.ts
+++ b/engine/runtime/commands/src/runtime/runtime.ts
@@ -94,6 +94,8 @@ function runtimeSet (opts: RuntimeCommandOptions, params: string[]): void {
   if (opts.global) {
     args.push('--global')
     if (opts.bin) args.push('--global-bin-dir', opts.bin)
+  } else {
+    args.push('--ignore-workspace-root-check')
   }
   if (opts.storeDir) args.push('--store-dir', opts.storeDir)
   if (opts.cacheDir) args.push('--cache-dir', opts.cacheDir)
diff --git a/engine/runtime/commands/test/runtime.test.ts b/engine/runtime/commands/test/runtime.test.ts
index dcf6be67e3..685e47ab61 100644
--- a/engine/runtime/commands/test/runtime.test.ts
+++ b/engine/runtime/commands/test/runtime.test.ts
@@ -37,7 +37,7 @@ test('runtime set uses project dir when not global', async () => {
   }, ['set', 'node', '22'])
 
   expect(mockRunPnpmCli).toHaveBeenCalledWith(
-    ['add', 'node@runtime:22'],
+    ['add', 'node@runtime:22', '--ignore-workspace-root-check'],
     { cwd: '/tmp/project' }
   )
 })