Preheat the oven to 350F and place a rack in the center position.
In a mixing bowl, combine the almond flour, coconut flour, pumpkin spice, baking soda, baking powder, and salt. Whisk until combined and set aside. In a separate mixing bowl, combine the pumpkin puree, eggs, maple syrup, almond butter, coconut milk and vanilla. Whisk until smooth.
Pour the pumpkin mixture into the flour mixture and gently fold the ingredients together with a spatula until combined.
Line a 12-cup muffin tray with parchment paper cups. Using a spoon or ice cream scooper, evenly distribute the muffin mix. Gently tap the tray against your cutting board or counter to release any air pockets. Transfer to the preheated oven and bake until you can insert a cake tester into the center of each muffin and it comes out clean, around 30 minutes.
Transfer the muffins to a cooling rack and let them cool completely before serving. They can be stored, covered, in a refrigerator for up to 5 days.