Preheat the oven to 350°F (175°C). Line a baking sheet with parchment paper.
In a large bowl, whisk together the oat flour, vanilla whey 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, eggs, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined.
Add the almond milk and mix gently until the batter is smooth and thick.
Fold in the mini dark chocolate chips evenly throughout the batter.
Using a tablespoon or small ice cream scoop, drop heaping spoonfuls of batter onto the prepared baking sheet, spacing them about 2 inches apart. Flatten the tops slightly to form muffin tops.
Bake for 14 to 16 minutes, or until the tops are set and a toothpick inserted into the center comes out with a few moist crumbs.
Remove from the oven and allow the muffin tops to cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.
Serve warm or at room temperature.