CocoaPods pod init Fails with “Unknown ISA PBXFileSystemSynchronizedRootGroup” Error on Xcode 16

Question

I’m trying to initialize CocoaPods in a new iOS project using Xcode 16. When I run pod init, I get the following error:

RuntimeError - `PBXGroup` attempted to initialize an object with unknown ISA `PBXFileSystemSynchronizedRootGroup`

I’ve updated CocoaPods, Xcode, and xcodeproj, but the error still persists. Has anyone else encountered this issue with Xcode 16, and how did you resolve it?

Environment:

•   Xcode 16.0
•   CocoaPods: 1.15.2
•   macOS 15.0

Command

/usr/local/bin/pod init

Stack

   CocoaPods : 1.15.2
        Ruby : ruby 2.6.10p210 (2022-04-12 revision 67958) [universal.x86_64-darwin24]
    RubyGems : 3.0.3.1
        Host : macOS 15.0 (24A5331b)
       Xcode : 16.0 (16A242)
         Git : git version 2.39.5 (Apple Git-154)
Ruby lib dir : /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib
Repositories : trunk - CDN - https://cdn.cocoapods.org/

Error

RuntimeError - `PBXGroup` attempted to initialize an object with unknown ISA `PBXFileSystemSynchronizedRootGroup` from attributes: `{"isa"=>"PBXFileSystemSynchronizedRootGroup", "exceptions"=>["AE97BCA32C917722000D94D0"], "path"=>"tesPlayer", "sourceTree"=>"<group>"}`
If this ISA was generated by Xcode please file an issue: https://github.com/CocoaPods/Xcodeproj/issues/new

Answer 1

In Xcode, right-click on the BLUE folders, select Convert to Group from the context menu, and then it can be used normally.

This is because in Xcode 16, it defaults to folders instead of groups. The Cocoapods version you're using isn't able to process that nicely. For more on that see here

Answer 2

I am facing same issue in iOS 18.0 and XCode 16

Note: Before this step try @zhaozhang solution if it not resolved problem Then Try this step by step it will be resolved.

• Close XCode
• Go to your project folder remove Pods & Podfile.lock
• Right Click on YOUR_PROJECT_NAME.xcodeproj Show Package Contents then open project.pbxproj
• Replace every PBXFileSystemSynchronizedRootGroup with PBXGroup
• Search for objectVersion should be like that objectVersion = 56; if not replace by 56
• Pod install

Enjoy:)

UPDATED

This solution will also work for pod init as well