Prepare the oven and muffin pan. Preheat the oven to 425°F (220°C). Line a standard 12-cup muffin pan with paper liners or lightly grease each cup.
Combine the dry ingredients. Add the all-purpose flour, whole wheat flour, vanilla protein powder, baking soda, baking powder, kosher salt, and pumpkin pie spice to a large mixing bowl. Whisk until evenly combined.
¾ cup all-purpose flour, ¾ cup whole wheat flour, ½ cup vanilla protein powder, 1½ teaspoons baking soda, ½ teaspoon baking powder, ½ teaspoon kosher salt, 2 teaspoons pumpkin pie spice
Mix the wet ingredients. In a separate bowl, whisk together the pumpkin puree, brown sugar, maple syrup, eggs, oil, Greek yogurt, and vanilla extract until smooth and well blended.
1 (15-ounce) can pumpkin puree, ½ cup light brown sugar, ¼ cup maple syrup, 2 large eggs, ¼ cup neutral oil, ¼ cup plain Greek yogurt, 2 teaspoons vanilla extract
Make the batter. Add the pumpkin mixture to the bowl with the dry ingredients. Using a spatula, gently fold everything together just until no large pockets of dry flour remain. Avoid overmixing.
Fill the muffin pan. Spoon the batter evenly into the prepared muffin cups, filling each approximately three-quarters full. Sprinkle the pepitas over the tops just before the muffins go into the oven.
¼ cup pepitas
Bake at two temperatures. Bake at 425°F (220°C) for 5 minutes. Without opening the oven door, lower the temperature to 350°F (175°C). Continue baking for another 15-20 minutes, until the tops are golden and a toothpick inserted into the center of a muffin comes out clean.
Cool. Allow the muffins to cool in the pan for about 5 minutes. Transfer them to a wire rack and let them finish cooling before serving.