Prep the pan and oven: Heat your oven to 350°F (175°C).
Line a 12-cup muffin pan with paper liners or lightly grease it.
Mash the bananas: In a large bowl, mash the ripe bananas with a fork until mostly smooth. A few small lumps are fine.
Whisk the wet ingredients: Add eggs, oil, vanilla, brown sugar, and yogurt (or milk) to the bananas. Whisk until the mixture looks smooth and glossy.
If using honey or maple syrup, whisk it in now.
Combine the dry ingredients: In a separate bowl, whisk together whole-wheat flour, baking powder, baking soda, salt, and cinnamon.
Bring it together: Add the dry ingredients to the wet mixture. Stir gently with a spatula just until you no longer see streaks of flour. The batter should be thick and slightly lumpy.
Avoid overmixing.
Fold in add-ins: If using nuts, chocolate chips, or berries, fold them in now. About 1/2 to 3/4 cup total add-ins works well.
Rest the batter (optional but helpful): Let the batter sit for 5–8 minutes. This gives the whole-wheat flour time to hydrate for a softer crumb.
Fill the cups: Divide the batter evenly among the muffin cups, filling them about 3/4 full.
For bakery-style domes, you can fill a little higher.
Bake: Bake for 16–20 minutes, or until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs.
Cool: Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack. Serve warm or at room temperature.