Preheat oven to 425 degrees Fahrenheit. Spray a 12-count muffin pan well with nonstick cooking spray and set aside.
In a large bowl, whisk together the flour, baking powder, baking soda, salt, cocoa powder, and chocolate chip.
In a separate bowl, mix together the Greek yogurt, brown sugar, honey, milk, oil, egg, and vanilla.
Add the wet ingredients to the dry ingredients and mix until just combined.
Evenly distribute the batter between all 12 muffin cavities.
Bake at 425 degrees for 5 minutes, reduce the temperature to 375 degrees (do not remove the muffins from the oven) and continue baking for an additional 10 minutes or until a toothpick inserted into the center comes out clean.
Allow to cool in the pan for about 5 minutes, then remove from the muffin pan to a wire rack to finish cooling.