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

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/libRepositories : 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