Prep the pan and oven: Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease well.
Make oat flour if needed: If using rolled oats, blend 1 cup in a blender until fine and sandy.
Measure after blending to ensure accuracy.
Whisk the dry mix: In a large bowl, whisk 3/4 cup oat flour, 3/4 cup all-purpose flour, 1/2 cup cocoa powder, 1/2 cup chocolate protein powder, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, and 1/2 teaspoon salt. Add 1 teaspoon espresso powder if using.
Combine the wet ingredients: In a separate bowl or measuring cup, whisk 3/4 cup Greek yogurt, 1/2 cup milk, 2 large eggs, 1/4 cup oil, 1 teaspoon vanilla, 1/3 cup honey or maple syrup, and 1/4 cup brown sugar until smooth.
Bring it together: Pour the wet mixture into the dry ingredients. Stir gently with a spatula until just combined.
The batter should be thick but scoopable. Avoid overmixing.
Fold in chocolate: Stir in 1/2 to 3/4 cup chocolate chips, reserving a small handful for topping.
Fill the cups: Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full. Sprinkle the reserved chips on top for a bakery-style look.
Bake: Bake for 16–20 minutes, or until the tops spring back and a toothpick comes out with a few moist crumbs (melted chocolate is fine).
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This prevents soggy bottoms.
Enjoy: Serve warm or at room temperature. For extra decadence, add a small pinch of flaky salt on top.