Preheat oven to 400 degrees Fahrenheit. Grease the cups of a 24-cup mini muffin pan with a little coconut oil or an oil mister. Set aside.
In a large bowl, whisk together the applesauce, peanut butter, and honey until well-blended. Stir in the coconut oil. Add the egg and whisk well. Stir in the vanilla and quinoa.
In a medium bowl, whisk together the flour, baking powder, cinnamon, nutmeg, and salt. Pour the dry ingredients over the wet ingredients and mix with a whisk or wooden spoon just until blended. Stir in the chocolate chips, if using.
*If you're adding chocolate chips to only half, fill 12 of the muffin cups with the plain batter (about a scant 2 tablespoons each). Then stir in 1/4 cup chocolate chips to the remaining batter and divide the chocolate chip batter among the remaining cups.
Bake until the tops spring back when you gently poke them with your finger, 9-10 minutes.
Remove from oven and let cool for about 5 minutes. Remove from tins and place on a wire rack to cool for another 5 minutes. Serve. Muffins keep in an airtight container for 3-4 days. They also freeze well.
This also adapts well to standard-size muffins. I find I get about 10 good-size muffins and they take about 14-15 minutes to bake.