diff --git a/src/install/PackageManager/PackageManagerOptions.rs b/src/install/PackageManager/PackageManagerOptions.rs
index da7ddb805c55..038b88070f20 100644
--- a/src/install/PackageManager/PackageManagerOptions.rs
+++ b/src/install/PackageManager/PackageManagerOptions.rs
@@ -631,6 +631,30 @@ impl Options {
             }
         }
 
+        if let Some(cli) = &maybe_cli {
+            if !cli.registry.is_empty() {
+                let new_url = bun_url::URL::parse(cli.registry);
+                let same_origin = {
+                    let prev_url = self.scope.url.url();
+                    bun_core::without_trailing_slash(new_url.host)
+                        == bun_core::without_trailing_slash(prev_url.host)
+                        && (new_url.is_https() || !prev_url.is_https())
+                };
+                if !same_origin {
+                    self.scope.token = Box::default();
+                    self.scope.auth = Box::default();
+                    self.scope.user = Box::default();
+                }
+                let href: Box<[u8]> = cli.registry.into();
+                self.scope.url_hash =
+                    Npm::registry::Scope::hash(bun_core::without_trailing_slash(&href));
+                self.scope.url = bun_url::OwnedURL::from_href(href);
+            }
+        }
+
+        // Unlike the credentials dropped by the registry overrides above, these
+        // are not tied to a host: they apply to whichever registry ended up as
+        // the default, so they are read only once that is settled.
         {
             const TOKEN_KEYS: [&[u8]; 3] = [
                 b"BUN_CONFIG_TOKEN",
@@ -687,25 +711,6 @@ impl Options {
             self.enable
                 .set(Enable::ONLY_MISSING, cli.only_missing || cli.analyze);
 
-            if !cli.registry.is_empty() {
-                let new_url = bun_url::URL::parse(cli.registry);
-                let same_origin = {
-                    let prev_url = self.scope.url.url();
-                    bun_core::without_trailing_slash(new_url.host)
-                        == bun_core::without_trailing_slash(prev_url.host)
-                        && (new_url.is_https() || !prev_url.is_https())
-                };
-                if !same_origin {
-                    self.scope.token = Box::default();
-                    self.scope.auth = Box::default();
-                    self.scope.user = Box::default();
-                }
-                let href: Box<[u8]> = cli.registry.into();
-                self.scope.url_hash =
-                    Npm::registry::Scope::hash(bun_core::without_trailing_slash(&href));
-                self.scope.url = bun_url::OwnedURL::from_href(href);
-            }
-
             if let Some(cache_dir) = cli.cache_dir {
                 self.cache_directory = cache_dir;
             }
diff --git a/test/cli/install/config-precedence.test.ts b/test/cli/install/config-precedence.test.ts
index c5d77e070fcf..8daaf166eb9b 100644
--- a/test/cli/install/config-precedence.test.ts
+++ b/test/cli/install/config-precedence.test.ts
@@ -528,6 +528,38 @@ describe.concurrent("bun install config precedence", () => {
     expect(exitCode).toBe(0);
   });
 
+  test.each(["BUN_CONFIG_TOKEN", "NPM_CONFIG_TOKEN"])(
+    "%s applies to the registry passed with --registry",
+    async key => {
+      using capture = capturingRegistry();
+      using dir = tempDir("config-precedence", {
+        "project/package.json": packageJson({ "@needs-auth/test-pkg": "1.0.0" }),
+      });
+      const { stderr, exitCode } = await install(String(dir), ["--registry", capture.url], { [key]: authToken });
+      expect(stderr).not.toContain("error:");
+      expect(new Set(capture.authorizations)).toStrictEqual(new Set([`Bearer ${authToken}`]));
+      expect(installed(String(dir), "@needs-auth", "test-pkg")).toBe(true);
+      expect(exitCode).toBe(0);
+    },
+  );
+
+  test("--registry drops the _authToken of the .npmrc registry but keeps BUN_CONFIG_TOKEN", async () => {
+    using dead = deadRegistry();
+    using capture = capturingRegistry();
+    using dir = tempDir("config-precedence", {
+      "project/.npmrc": `registry=${dead.url}\n//localhost:${dead.server.port}/:_authToken=token-for-dead\n`,
+      "project/package.json": packageJson({ "@needs-auth/test-pkg": "1.0.0" }),
+    });
+    const { stderr, exitCode } = await install(String(dir), ["--registry", capture.url], {
+      BUN_CONFIG_TOKEN: authToken,
+    });
+    expect(stderr).not.toContain("error:");
+    expect(dead.hits).toBe(0);
+    expect(new Set(capture.authorizations)).toStrictEqual(new Set([`Bearer ${authToken}`]));
+    expect(installed(String(dir), "@needs-auth", "test-pkg")).toBe(true);
+    expect(exitCode).toBe(0);
+  });
+
   test("NPM_CONFIG_REGISTRY beats registry= in project .npmrc", async () => {
     using dead = deadRegistry();
     using dir = tempDir("config-precedence", {