Preheat the oven to 350 degrees and line a 12-cup muffin tray with paper liners.
In a large bowl, combine flaxseed, mashed banana, coconut oil, milk, brown sugar, and vanilla. Whisk well and set aside.
In a small bowl, combine flours, baking soda, baking powder, cocoa powder and salt. Add dry ingredients to the wet ingredients, folding gently to just combine. It is okay if there are some dry spots. Fold in chocolate chips.
Divide the mixture between the 12 muffin cups and bake at 350 for 18-20 minutes. Muffins will be springy to the touch or pass the toothpick test.