Preheat the oven to 350°F (175°C). Line a baking sheet with parchment paper.
In a large bowl, whisk together oat flour, vanilla protein powder, cocoa powder, baking powder, baking soda, and salt until well combined.
In a separate medium bowl, mix the applesauce, maple syrup, Greek yogurt, egg, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined.
Gradually add the almond milk and mix until the batter is smooth and thick.
Fold in the mini dark chocolate chips gently.
Using a tablespoon or ice cream scoop, drop batter onto the prepared baking sheet, spacing them about 2 inches apart. Flatten each slightly to form muffin tops.
Bake for 14 to 16 minutes, or until the tops are set and a toothpick inserted in the center comes out clean.
Remove from oven and let cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.