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Can't transfer purchases from iPhone to iTunes in iOS 9

After upgrading to iOS 9, I can't transfer purchases from my iPhone to iTunes. It happens to just start the process, then it finishes without transferring anything. However, I can still transfer purchases from my iPad with iOS 8.4 like before.

  • iPhone 5c, iOS 9
  • iTunes 12.3
  • MacBook Pro 13" with Retina Display Mid 2014, OS X El Capitan

Apparently, not many people happen to use this "transfer purchases" feature so it didn't get any real attention. I used it a lot, I used to update my apps on my iPhone, transfer them to iTunes and updated my iPad apps using iTunes. Still, I can update my apps using iTunes and update apps on all my devices.

Answer