Preheat the oven to 325 degrees Fahrenheit.
Place the eggs, pumpkin puree, vanilla, sweetener, and almond milk in a large bowl. Mix thoroughly using a hand-held or standing mixer.
In another bowl, whisk together the almond flour, coconut flour, salt, baking powder, and pumpkin pie spice.
Add the wet ingredients to the dry and combine well with a mixer or spatula.
Pour in 1/2 cup of the sugar-free chocolate chips. Save the rest to sprinkle on top.
Prepare a muffin tin with liners or grease with butter. Place 2 tablespoons of batter in the bottom of each muffin tin round.