In the bowl of a stand mixer fitted with the paddle attachment, beat the cream cheese and sugar together until smooth and creamy. Place in the refrigerator until ready to use.

Preheat oven to 425ºF. Spray a standard-sized muffin pan with non-stick cooking spray, or line with paper liners.

In a medium saucepan, melt the butter over medium-low heat. Once melted, turn off the heat and stir in the cocoa powder. Allow to cool for at least 5 minutes.

In a large bowl, whisk together the flour, baking powder, baking soda, and salt until combined; set aside.

In another bowl, whisk both sugars and the eggs together until thickened and combined, about 45 seconds. Whisk in the melted butter-cocoa mixture and the oil. Add the yogurt and vanilla, and continue whisking until combined. Blend in food coloring until desired shade is achieved.

Using a rubber spatula, gently fold the wet ingredients into the dry ingredients until almost combined. Pour in the chocolate chips, folding until just combined. Batter should still be lumpy with a few spots of flour.

Fill each muffin well with a heaping tablespoon of batter, or just enough to cover the bottom of the pan/liner. Spoon a small dollop (about 2 teaspoons) into the center of each muffin well. Cover the cream cheese completely with more batter, filling muffin wells to nearly the top of the liner; there should only be about one centimeter of space at the top.

Bake at 425ºF for 5 minutes, then reduce the oven temperature to 375ºF and continue to bake for another 8-11 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs attached. Allow to cool in the pan for 10 minutes before serving.