Preheat oven to 400 degrees. Line a cupcake pan or muffin tin with paper liners or silicone baking cups. Set pan aside.
In a medium bowl, whisk together the dry ingredients; flour, protein powder, cocoa powder, baking powder, baking soda and salt. Set aside.
In large mixing bowl, whisk together the wet ingredients; yogurt, eggs, oil, granular sweetener and vanilla.
Gradually add the dry ingredients to the wet ingredients with a rubber scraper. The batter will become very thick, almost like brownie batter. Do your best to not overmix. Once ingredients are combined, fold in the chocolate chips.
Spoon the batter into the prepared pan, filling each muffin cup full.
Bake the muffins at 400 degrees for approximately 18 minutes. To test for doneness, insert a toothpick into the center of a muffin. If it comes out clean and crumb-free, the muffins are done.
Remove muffins from oven and let cool for 10-15 minutes before enjoying.