Prep the pan: Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Mix dry ingredients: In a large bowl, whisk oat flour, protein powder, baking powder, baking soda, and salt until combined.
Mix wet ingredients: In a separate bowl, whisk eggs, Greek yogurt, peanut butter, maple syrup, vanilla, and milk until smooth.
If your peanut butter is very thick, warm it slightly so it blends easily.
Combine: Pour the wet mixture into the dry ingredients. Stir gently with a spatula until just combined. Do not overmix; the batter should be thick but scoopable.
Add chocolate: Fold in most of the chocolate chips, reserving a tablespoon or two for the tops.
Fill the cups: Divide the batter evenly among the muffin cups (about 3/4 full).
Add a small dollop of peanut butter on each and swirl with a toothpick, if using. Sprinkle with remaining chocolate chips.
Bake: Bake for 16–20 minutes, or until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs. Avoid overbaking to keep them tender.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely.
They firm up as they cool.
Enjoy: Serve slightly warm for the best peanut butter cup experience as the chocolate melts.