Preheat oven to 375°F. Grease or line a mini muffin tin (I love this silicone one).
Combine flaxseed and warm water in a small bowl. Let sit for 5–10 minutes to thicken.
In a large bowl, combine mashed sweet potato, banana, cottage cheese, milk, avocado oil, maple syrup, flax egg, and vanilla. Stir until mostly smooth.
Add flour, whole wheat flour, baking powder, baking soda, and cinnamon. Stir gently until just combined. If using, stir in chocolate chips.
Divide batter evenly among 24 mini muffin cups. Bake for 14 minutes, or until a toothpick inserted in the center comes out clean.
Let cool for 5 minutes in the pan, then transfer to a wire rack.