Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or grease it lightly.
In a blender or food processor, pulse the rolled oats until they form a fine flour-like consistency.
In a large mixing bowl, combine the oat flour, vanilla protein powder, cocoa powder, baking powder, baking soda, and salt. Stir well to combine.
In a separate bowl, whisk together the eggs, unsweetened applesauce, honey, almond milk, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix.
Fold in the mini dark chocolate chips gently.
Spoon the batter evenly into the prepared muffin tin, filling each cup about 3/4 full to allow room for muffin tops to rise.
Bake for 13 to 15 minutes, or until a toothpick inserted into the center comes out clean and the tops are set and slightly firm.
Remove from the oven and let the muffin tops cool in the tin for 5 minutes before transferring to a wire rack to cool completely.
Serve warm or at room temperature.