After updating to El Capitan I stumbled upon a serious issue: I couldn’t update pods on my projects — the pod command could not be found. I had to find a way to re-install CocoaPods.
Simple solution — in a terminal, run:
sudo gem install -n /usr/local/bin cocoapods
The original command, sudo gem install cocoapods, did not work because of write permissions: since El Capitan, System Integrity Protection keeps /usr/bin read-only even for root, so gems have to land somewhere user-writable like /usr/local/bin — that’s what the -n flag does.
Reading this in 2026: SIP is still the reason, but the flag dance is obsolete on a modern Mac — install with Homebrew (brew install cocoapods) or pin it in the project’s Gemfile so the whole team runs the same version. The getting-started guide covers both, and the project is still actively maintained.