Preheat your oven to 350 degrees and spray a muffin tin with cooking spray.
In a medium bowl, stir together the flour cocoa powder, baking powder, baking soda, salt and Truvia until well mixed.
In a separate, large bowl whisk together ½ Cup + 2 Tbsp of the Greek yogurt, honey, egg, vanilla extract and almond milk.
Add the dry ingredients and chocolate chips to the wet ingredients, and still until just moistened, being careful not to over-mix.
In a small bowl, stir together the softened cream cheese and Truvia until well mixed.
Fill the muffin tins only ½ of the way full, making small depressions in the center of the batter. Drop ½ Tbsp of the cream cheese mixture into the center of each muffin, and lightly press down to flatten it. Cover with a spoon of remaining batter and gently spread to cover the cream cheese. Your muffin tin should only be able ¾ of the way full, or else your muffins will be too big and flatten *
Bake until a toothpick inserted in the center comes out clean, about 17-18 minutes. Be careful not to over-bake these as they go from perfect to dry quickly.
Let cool in the muffin tin for 10 mins and then transfer to a rack to finish cooling.