Prep the oven: Heat to 350°F (175°C). Line a 12-cup muffin tin or grease lightly.
Mix dry ingredients: In a large bowl, whisk flour, protein powder, baking powder, baking soda, salt, and pumpkin pie spice.
Mix wet ingredients: In a separate bowl, whisk pumpkin, eggs, Greek yogurt, maple syrup, milk, oil, and vanilla until smooth.
Combine gently: Pour wet into dry.
Stir with a spatula until just combined. If using add-ins, fold them in now. The batter will be thick.
Portion: Divide evenly among the muffin cups, filling each about 3/4 full.
Bake: 16–20 minutes, until tops spring back and a toothpick comes out with a few moist crumbs.
Cool: Let sit in the pan 5 minutes, then transfer to a rack to cool completely for best texture.