1. Prepare Your Oven and Muffin Tin: Begin by preheating your oven to 375 F (190 C). While the oven heats, line a 12-cup muffin tin with paper liners or lightly grease each cup with cooking spray. This prevents sticking and makes for easy removal.

2. Mash the Bananas: In a large mixing bowl, thoroughly mash your ripe bananas with a fork until mostly smooth. A few small lumps are perfectly fine and can add nice texture to the finished muffins. The riper the bananas, the easier they will be to mash.

3. Combine Wet Ingredients: To the mashed bananas, add the eggs, unsweetened applesauce, milk, and vanilla extract. Whisk these ingredients together until they are well combined and the mixture is smooth. Ensure there are no streaks of egg yolk remaining.

4. Mix Dry Ingredients Separately: In a separate medium bowl, whisk together the whole wheat flour, vanilla protein powder, brown sugar, baking soda, baking powder, ground cinnamon, and salt. Make sure to break up any clumps of brown sugar or protein powder to ensure even distribution.

5. Combine Wet and Dry Mixtures: Pour the dry ingredients into the wet ingredients. Using a spatula or wooden spoon, gently mix until just combined. Be careful not to overmix the batter; overmixing can lead to tough muffins. A few lumps of flour are acceptable. If using, gently fold in the chocolate chips at this stage.

6. Fill Muffin Cups: Divide the batter evenly among the 12 prepared muffin cups. Each cup should be about two-thirds full. An ice cream scoop can be helpful for this step to ensure uniform muffin sizes.

7. Bake Until Golden: Place the muffin tin in the preheated oven and bake for 18-22 minutes. The muffins are done when they are golden brown on top and a wooden skewer or toothpick inserted into the center of a muffin comes out clean or with only a few moist crumbs attached.

8. Cool Before Serving: Once baked, remove the muffin tin from the oven and let the muffins cool in the tin for 5 minutes. Then, transfer them to a wire rack to cool completely. This helps prevent them from becoming soggy and allows them to set properly.