Preheat oven to 350°F. Line a 12-cup muffin pan with parchment liners or grease cups. Whisk almond flour, coconut flour, baking soda, pumpkin pie spice, and salt in a large bowl.

In another bowl, whisk eggs, pumpkin puree, maple syrup, melted coconut oil, vanilla, and apple cider vinegar until smooth.

Pour wet mixture into dry ingredients and fold with a spatula just until combined. Batter will be thick.

Divide batter evenly among muffin cups, filling each about three-quarters full. Bake 18–22 minutes until a toothpick inserted in the center comes out clean.

Cool muffins in the pan for 5 minutes, then transfer to a wire rack. Serve warm or at room temperature.