Since the accepted answer's side effects have been removed by a script written by Kyle Fuller - deintegrate, I'll post the proper workflow here:

  1. Install deintegrate and clean:

    $ sudo gem install cocoapods-deintegrate
    $ sudo gem install cocoapods-clean
  2. Run deintegrate in the folder of the project:

    $ pod deintegrate

  3. Clean:

    $ pod clean

  4. Modify your podfile (delete the lines with the pods you don't want to use anymore) and run:

    $ pod install

Done.

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