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Preheat oven to 425°F (218°C). Spray 12-count muffin pan with nonstick spray. If using cupcake liners, spray those lightly with nonstick spray. Set aside.
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.