Start by preheating the oven to 375F and lining a muffin tray with liners, either paper or silicone.
Whisk together in a smaller bowl, the flour, cocoa powder, baking powder, baking soda, and salt. Set aside.
Use a stick blender of food processor to blend the cottage cheese, as smooth as possible.
Transfer the blended cottage cheese to a large mixing bowl. Add the brown sugar and eggs to the cottage cheese and whisk until smooth.
Pour the milk, vanilla, and canola oil into the wet ingredients and mix until incorporated.
Add all of the dry ingredients and the chocolate chips, to the wet ingredients. Use a rubber spatula to fold the the batter until there is no more dry flour mixture. Make sure to not overmix the batter.
Divide the batter between the 12 prepared muffin cavities. Notice that the batter should almost fill each liner. Place a couple of extra chocolate chips or shaved baking chocolate on top for an optional boost of chocolate.
Bake the Chocolate Cottage Cheese Muffins in the preheated 375F oven for 20-25 minutes. The muffins are ready when a toothpick, inserted in the middle comes out clean. Cool the muffins or 10-15 minutes to help them set before eating.