Bake for 5 minutes at 425°F (218°C). Keeping the muffins in the oven, reduce the temperature down to 375°F (191°C) and continue to bake for 13 more minutes. Insert a toothpick into the center of one muffin. If it comes out clean, they’re done.
In a large bowl, combine pumpkin, brown sugar, maple syrup, egg whites, greek yogurt, oil, and vanilla extract. Whisk them all together until smooth, with no yogurt lumps remaining.
Sift the flours, cocoa powder, salt, baking soda, baking powder, cinnamon, and pumpkin pie spice together into a large bowl. Slowly stir in the wet ingredients, being careful not to overmix. Get any dry pockets of flour out. Fold in the mini chocolate chips. The batter will be a little chunky and extremely, extremely thick.
Divide the batter evenly among the muffin cups—fill them all the way to the top if you can. If desired, sprinkle a few more mini chocolate chips on top before baking.
Bake for 5 minutes at 425°F (218°C). Keeping the muffins in the oven, reduce the temperature down to 375°F (191°C) and continue to bake for 13 more minutes. Insert a toothpick into the center of one muffin. If it comes out clean, they’re done.
Remove from the oven and allow to cool for 5 minutes in the pan, then transfer to a wire rack to cool completely.
Muffins stay fresh in an airtight container at room temperature for up to 1 week.