Preheat over to 350 degrees F and lightly spray a muffin tray with non-stick cooking spray or line with paper liners.
Add the applesauce, almond butter (or melted coconut oil) and maple syrup to mixing bowl and mix until smooth and creamy.
Add the flour, oats, cinnamon, salt, baking powder, ground flax and protein powder. While the dry ingredients are sitting on top of the wet ingredients, gently mix to help distribute the baking powder and salt. Mix into the wet ingredients until all of the dry ingredients have been wetted. Avoid over-mixing.
Fold in the chocolate chips until evenly distributed throughout the batter.
Spoon the mixture into the 12 cups of the muffin tin. The batter should come just slightly below the top of each cup. Bake for 26-30 minutes. Check at 26 minutes, they should be baked through, it just depends how hard and crunchy you want the outside. They should be fairly browned after 25 minutes but you can leave them up to 30 if you want them a bit crispier.
After baking, use a knife to gently pop the muffins out of the pan and onto a cooling rack. Let cool completely before storing. Once cool, muffins can be stored in an airtight container at room temperature for 3-4 days, in the fridge for at least 1 week or frozen for 3 months.