diff --git a/scopes/dependencies/dependency-resolver/manifest/workspace-manifest-factory.ts b/scopes/dependencies/dependency-resolver/manifest/workspace-manifest-factory.ts
index b80ab47e82b4..55956dd9ef97 100644
--- a/scopes/dependencies/dependency-resolver/manifest/workspace-manifest-factory.ts
+++ b/scopes/dependencies/dependency-resolver/manifest/workspace-manifest-factory.ts
@@ -115,6 +115,11 @@ export class WorkspaceManifestFactory {
   }
 
   private getEnvsSelfPeersPolicy(componentsManifestsMap: ComponentsManifestsMap) {
+    // When using external package manager, skip collecting env self peers.
+    // Users manage their own tooling dependencies.
+    if (this.dependencyResolver.config.externalPackageManager) {
+      return undefined;
+    }
     const foundEnvs: EnvPolicy[] = [];
     for (const component of componentsManifestsMap.values()) {
       foundEnvs.push(component.envPolicy);
@@ -243,6 +248,12 @@ export class WorkspaceManifestFactory {
     component: Component,
     packageNamesFromWorkspace: string[]
   ): Promise<Record<string, string>> {
+    // When using external package manager, don't add env's tooling dependencies to components.
+    // The user manages their own tooling (eslint, vitest, webpack, etc.) and we should only
+    // include the component's actual source code dependencies (detected from imports).
+    if (this.dependencyResolver.config.externalPackageManager) {
+      return {};
+    }
     const envPolicy = await this.dependencyResolver.getComponentEnvPolicy(component);
     const selfPolicyWithoutLocal = envPolicy.selfPolicy.filter(
       (dep) => !packageNamesFromWorkspace.includes(dep.dependencyId)
diff --git a/scopes/workspace/install/install.main.runtime.ts b/scopes/workspace/install/install.main.runtime.ts
index 17a7402f71f6..96103bfcc0b0 100644
--- a/scopes/workspace/install/install.main.runtime.ts
+++ b/scopes/workspace/install/install.main.runtime.ts
@@ -229,7 +229,11 @@ export class InstallMain {
   async writeDependenciesToPackageJson(): Promise<void> {
     const installer = this.dependencyResolver.getInstaller({});
     const mergedRootPolicy = await this.addConfiguredAspectsToWorkspacePolicy();
-    await this.addConfiguredGeneratorEnvsToWorkspacePolicy(mergedRootPolicy);
+    // When using external package manager, don't add the env package itself.
+    // Users don't need the env installed - they manage their own tooling.
+    if (!this.dependencyResolver.config.externalPackageManager) {
+      await this.addConfiguredGeneratorEnvsToWorkspacePolicy(mergedRootPolicy);
+    }
     const componentsAndManifests = await this._getComponentsManifests(installer, mergedRootPolicy, {
       dedupe: true,
     });
diff --git a/scopes/workspace/workspace/workspace.ts b/scopes/workspace/workspace/workspace.ts
index 0f27b4c21547..4129a18d26a7 100644
--- a/scopes/workspace/workspace/workspace.ts
+++ b/scopes/workspace/workspace/workspace.ts
@@ -2508,7 +2508,14 @@ the following envs are used in this workspace: ${uniq(availableEnvs).join(', ')}
       ? Object.entries(dependencies).map(([name, currentRange]) => ({ name, currentRange }))
       : await this.getAllDedupedDirectDependencies();
     pkgJson.packageJsonObject.dependencies ??= {};
+    const existingDeps = pkgJson.packageJsonObject.dependencies;
+    const existingDevDeps = pkgJson.packageJsonObject.devDependencies ?? {};
+    const existingPeerDeps = pkgJson.packageJsonObject.peerDependencies ?? {};
     for (const dep of allDeps) {
+      // Skip if already exists - don't override user's existing dependency versions
+      if (existingDeps[dep.name] || existingDevDeps[dep.name] || existingPeerDeps[dep.name]) {
+        continue;
+      }
       pkgJson.packageJsonObject.dependencies[dep.name] = dep.currentRange;
     }
     await pkgJson.write();