Prep your pan: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or grease lightly.
Mix wet ingredients: In a large bowl, whisk 1 cup pumpkin puree, 2 eggs, 1/2 cup Greek yogurt, 1/3 cup milk, 1/4 cup oil, 1/4 cup maple syrup, 1/4 cup brown sugar, and 1 teaspoon vanilla until smooth.
Stir in protein: Add 1/2 to 3/4 cup protein powder.
Start with 1/2 cup; you can adjust later for batter thickness. Whisk until fully incorporated.
Combine dry ingredients: In a separate bowl, stir 1 cup whole wheat flour, 1/2 cup oat flour (or more whole wheat), 1 teaspoon baking powder, 1/2 teaspoon baking soda, 1 teaspoon cinnamon, 1 teaspoon pumpkin pie spice, and 1/2 teaspoon salt.
Bring it together: Add the dry ingredients to the wet. Fold gently until just combined.
If using add-ins, fold in 1/2 cup chocolate chips or nuts now. The batter should be thick but scoopable. If it seems too loose, add 2–3 tablespoons flour.
If too thick, splash in 1–2 tablespoons milk.
Fill the cups: Divide batter evenly among the muffin cups, filling about 3/4 full. Sprinkle tops with oats or pepitas for crunch if you like.
Bake: Bake 16–20 minutes, until the tops spring back and a toothpick comes out with a few moist crumbs. Avoid overbaking to keep them soft.
Cool: Let muffins cool in the pan 5 minutes, then move to a rack to cool completely.
This helps set the structure and keeps the bottoms from steaming.