diff --git a/src/commands.ts b/src/commands.ts
index 3007a33..b51140d 100644
--- a/src/commands.ts
+++ b/src/commands.ts
@@ -84,6 +84,16 @@ export async function setupBunfigToml(dir: string) {
   }
 }
 
+async function bunfigExists(dir: string): Promise<boolean> {
+  const bunfigPath = path.join(dir, BUNFIG_FILE);
+  try {
+    await fs.promises.access(bunfigPath);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
 export interface BaseOptions {
   pkgManagerName: PkgManagerName | null;
 }
@@ -99,11 +109,21 @@ export async function install(packages: JsrPackage[], options: InstallOptions) {
   );
 
   if (packages.length > 0) {
-    if (pkgManager instanceof Bun && !(await pkgManager.isNpmrcSupported())) {
-      // Bun v1.1.17 or lower doesn't support reading from .npmrc
-      // Bun v1.1.18+ supports npmrc
-      // https://bun.sh/blog/bun-v1.1.18#npmrc-support
-      await setupBunfigToml(root);
+    if (pkgManager instanceof Bun) {
+      // Always check if bunfig.toml exists first, regardless of Bun version
+      if (await bunfigExists(root)) {
+        // If bunfig.toml exists, use it
+        await setupBunfigToml(root);
+      } else if (!(await pkgManager.isNpmrcSupported())) {
+        // Bun v1.1.17 or lower doesn't support reading from .npmrc
+        // Bun v1.1.18+ supports npmrc
+        // https://bun.sh/blog/bun-v1.1.18#npmrc-support
+        // Create bunfig.toml for older versions
+        await setupBunfigToml(root);
+      } else {
+        // For newer Bun versions without existing bunfig.toml, use .npmrc
+        await setupNpmRc(root);
+      }
     } else if (pkgManager instanceof YarnBerry) {
       // Yarn v2+ does not read from .npmrc intentionally
       // https://yarnpkg.com/migration/guide#update-your-configuration-to-the-new-settings