Heat oven to 375 degrees. Prepare muffin pan with muffin cups or non-stick cooking spray.
In a small bowl, combine oats, flour, baking powder, salt, brown sugar, and flax seed. Stir to combine. Set aside.
In a large mixing bowl, combine peanut butter, coconut oil, vanilla, eggs, and milk. Use a hand mixer to cream the mixture together.
Add half of dry mixture to the wet mixture in the large mixing bowl. Blend them together and add the rest of the dry mix. This will keep the flour mixture from flying around too much when you mix it in.
When those are well combined, add the chocolate chips and mix in by hand.
Scoop the batter into the prepared muffin pan and bake at 375 for 15 - 20 minutes until the muffins are set and golden brown on top. A toothpick inserted in the center will come out clean.
Remove the muffins from the pan immediately and allow to cool on cooling rack about 5 minutes before serving.