Preheat your oven to 350°F (175°C) and line a mini muffin tin with paper liners or spray with non-stick cooking spray.
In a medium bowl, whisk together the flour, cocoa powder, baking soda, and salt until well combined.
In a large bowl, mix the granulated sugar, brown sugar, applesauce, vegetable oil, eggs, and vanilla extract until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Be careful not to overmix.
Fold in the chocolate chips until evenly distributed throughout the batter.
Spoon the batter into the prepared mini muffin tin, filling each cup about 2/3 full.
Bake for 10-12 minutes or until a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.