Preheat the oven to 375°F. Spray a standard muffin tin with nonstick baking spray.
In a large bowl whisk the applesauce, yogurt, egg, maple syrup, sugar, and vanilla until well combined and smooth. Add the flours, cocoa powder, salt, baking soda, and baking powder. Stir the batter with a rubber spatula until everything is well combined, but do not overmix, the batter may be lumpy but that’s okay. Stir in the chocolate chips.
Divide the batter between the muffin tin cups. Bake for 20 minutes. Transfer to a wire rack to cool. Serve warm or at room temperature. Store leftover muffins in an airtight container at room temperature for up to 3 days or freeze for up to two months. Microwave for 30 seconds to 1 minutes to reheat.