Preheat oven to 350 degrees F. Line muffin tin with liners and spray with cooking spray. Set aside.
In a large mixing bowl, whisk the eggs. Add applesauce, milk, maple syrup, coconut oil, vanilla and whisk well to combine. Add cacao powder, baking soda, baking powder, cinnamon and whisk until combined.
Add coconut flour and stir well. Add chocolate chips and cherries; give a few gentle stirs to incorporate.
Using large scoop, divide batter between 12 openings. Bake for 25 minutes or until toothpick inserted in the middle comes out sort of clean.
Remove from the oven and let cool for 10-15 minutes. Transfer to a cooling rack and let muffins cool off another 15 minutes to firm up.
Notes
Store: Store in a cool dry place for up to 3 - 4 days
Freeze: Airtight container up to 3 months.
Cherries: A few readers have reported using dried cherries successfully. Probably around half amount of fresh.
Liners: I highly recommend to use liners as coconut flour muffins are delicate.