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 the bananas until mostly smooth with a few small lumps. You should have around 1 1/4 cups.

Whisk in the wet ingredients. Add eggs, Greek yogurt, maple syrup (or honey), oil, and vanilla. Whisk until the mixture looks smooth and creamy.

Combine the dry ingredients. In a separate bowl, stir together whole-wheat pastry flour, almond flour, protein powder, baking soda, baking powder, cinnamon, and salt. Break up any clumps, especially in the almond flour and protein powder.

Bring it together. Add the dry ingredients to the wet bowl. Stir with a spatula until just combined. The batter should be thick but scoopable. Do not overmix.

Fold in the nuts. Gently fold in chopped walnuts or pecans and any optional mix-ins. Save a small handful of nuts for topping if you like a crunchy lid.

Portion the batter. Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full. Sprinkle extra nuts on top.

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. Protein-enriched batters can go from done to dry quickly, so start checking at 16 minutes.

Cool properly. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack. Cooling helps them set and prevents soggy bottoms.

Enjoy or store. Serve warm or at room temperature. Once fully cool, store as directed below.