Preheat oven to 350 F (180 C). Lightly grease 8 cups of a muffin tin with coconut oil. Set aside.
In medium bowl, whisk together almond flour, coconut flour, baking powder, salt, pepper, and 3 Tbsp (45 mL) pumpkin seeds.
In another medium bowl, whisk together eggs, pumpkin purée, rosemary, thyme, and sage. Stir in dry ingredients until fully incorporated. Divide batter among prepared muffin cups and sprinkle tops of muffins with remaining pumpkin seeds and Parmesan cheese.
Bake until wooden skewer inserted into a muffin comes out clean, about 30 minutes. Let muffins cool in pan for a couple of minutes before transferring to cooling rack to cool completely.
Each muffin contains: 162 calories; 9 g protein; 10 g total fat (2 g sat. fat, 0 g trans fat); 11 g total carbohydrates (3 g sugars, 4 g fiber); 192 mg sodium