Prep the oven and pan: Preheat to 350°F (175°C).
Line a 12-cup muffin tin with liners or lightly spray with oil.
Whisk the wet ingredients: In a large bowl, whisk 1 cup pumpkin puree, 2 large eggs, 1/2 cup plain Greek yogurt (or blended cottage cheese), and 1 teaspoon vanilla until smooth.
Combine the dry ingredients: In another bowl, mix 1 cup almond flour, 1/2 to 3/4 cup protein powder (start with 1/2 cup), 1/2 cup granulated sweetener, 1 1/2 teaspoons baking powder, a small pinch of baking soda, 1 to 1 1/2 tablespoons pumpkin pie spice, and 1/4 teaspoon salt.
Bring it together: Add dry ingredients to the wet and stir gently until just combined. If the batter seems too thick, add 1–3 tablespoons milk or water. If too thin, sprinkle in a little extra almond flour.
Add extras: Fold in 1/4 cup sugar-free chocolate chips or chopped nuts if using.
Don’t overmix.
Fill the tin: Divide the batter evenly among muffin cups. For a crunchy top, mix a teaspoon of sweetener with a pinch of cinnamon and sprinkle lightly.
Bake: Bake 16–20 minutes, or until the tops spring back lightly and a toothpick comes out mostly clean with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then move to a rack to cool completely. This helps set the structure.