Preheat oven to 350 degrees Fahrenheit (175 degrees Celsius) and grease a standard 12-cup muffin tin with non-stick spray.

In a high-speed blender, process the rolled oats until they reach a fine, flour-like consistency.

In a large mixing bowl, whisk together the processed oat flour, whey protein powder, baking powder, and baking soda.

In a separate bowl, whisk the eggs, then incorporate the applesauce, Greek yogurt, almond milk, and vanilla extract until the mixture is homogenous.

Pour the wet ingredients into the dry ingredients and fold gently with a spatula until just combined; avoid over-mixing to prevent a rubbery texture.

Gently fold the dark chocolate chips into the batter.

Distribute the batter evenly across the 12 muffin cups.

Bake for 18 to 22 minutes, or until an inserted toothpick emerges clean from the center.

Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.