Preheat your oven to 350°F (175°C). Line a muffin tin with parchment liners or silicone cups so the muffins release easily later. If using parchment liners, give them a very light spray of oil because high-protein muffins tend to stick more than regular muffins.
In a large mixing bowl, add the pumpkin puree, Greek yogurt, whole egg, egg whites, vanilla extract, and your preferred sweetener. Whisk everything together slowly at first, then more vigorously once it begins to combine. Keep whisking until the mixture looks smooth, creamy, and lump-free. If the yogurt or eggs were cold, the mixture may look slightly thick — this is normal.
In a separate medium bowl, whisk together the protein powder, almond or oat flour, baking powder, cinnamon, pumpkin pie spice, and a pinch of salt. Make sure the mixture looks evenly blended with no visible clumps, especially from the protein powder.
Pour the dry mixture into the wet mixture. Using a silicone spatula, gently fold the two together by scraping from the bottom of the bowl upward. Turn the bowl as you fold to keep the batter even. Stop as soon as you no longer see dry streaks — overmixing can make the muffins dense or rubbery.
Add the chocolate chips into the batter and fold gently until they are evenly distributed. Reserve a small handful of chips for the tops of the muffins — this gives them that bakery-style finish once baked.
Scoop the batter into the prepared muffin tin, filling each liner about three-quarters full. Try to divide the batter as evenly as possible so all muffins bake uniformly. Add the reserved chocolate chips on top of each portion, lightly pressing them into the batter.
Place the muffin tin into the preheated oven and bake for 18–23 minutes. Begin checking around the 18-minute mark. The muffins are ready when the tops look set and a toothpick inserted into the center comes out clean or with just a few moist crumbs. Avoid overbaking — high-protein muffins continue to cook slightly as they cool.
Remove the muffin tin from the oven and let the muffins cool in the pan for 10 minutes. This helps them firm up and prevents sticking. After 10 minutes, gently lift them out and transfer them to a cooling rack. Let them cool completely or enjoy warm. Store leftovers in an airtight container for meal prep.