I use digestive enzymes. If I don't, I get terrible indigestion and acid.

For proteins that are difficult to digest, I use one that has ox bile extract (just a quarter of a tablet though, because they are very powerful... sounds nasty, I know, but it's better than the indigestion). For fats, I use dried papaya (just an inch or so of the spear). My guess is that it's the fat in the pastry crust that is the problem, since apples, themselves, help to promote digestion.

If I use these, I almost never get indigestion, and I don't have to limit what kinds of foods I eat because of indigestion. I have to limit what I eat because of allergies, but that's another matter entirely.