Preheat your oven to 350°F (177°C) and line 10 muffin cups with parchment liners.
In a large bowl, combine coconut flour, almond flour, sweetener, baking powder, pumpkin pie spice, and sea salt, ensuring no clumps remain.
Add the eggs, pumpkin puree, almond milk, melted ghee, and vanilla, mixing until fully combined.
Distribute the batter evenly into the muffin cups, smoothing the tops. Fill them almost to the top and optionally sprinkle pumpkin seeds, pressing gently.
Bake for about 25 minutes, or until a toothpick inserted comes out clean and the edges are slightly golden.