Prep the pan and oven: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease each cup.
Mash the bananas: In a large bowl, mash ripe bananas until mostly smooth with a few small lumps.
Whisk in wet ingredients: Add eggs, maple syrup, Greek yogurt, oil, and vanilla.
Whisk until the mixture looks glossy and well combined.
Combine dry ingredients: In a separate bowl, whisk flour(s), cocoa powder, baking powder, baking soda, and salt to break up any lumps.
Bring it together: Add the dry mixture to the wet. Stir gently with a spatula until just combined. If the batter seems very thick, fold in 2–3 tablespoons of milk to loosen.
Do not overmix.
Add mix-ins: Fold in chocolate chips or nuts if using. Keep a few chips aside to sprinkle on top.
Fill the cups: Divide batter evenly among the 12 muffin cups, about three-quarters full. Sprinkle extra chips on top for a bakery look.
Bake: Bake 16–20 minutes, until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then move to a wire rack to cool completely.
The crumb sets as they cool.