Preheat the oven to 350°F (175°C). Lightly spray a standard muffin tray with cooking spray.
In a medium bowl, whisk together 1 cup (126 g) whole wheat flour, 1/2 cup unsweetened cocoa powder, 1 teaspoon baking powder, 1 teaspoon baking soda, 1/4 teaspoon sea salt, and 1/4 cup Truvia until evenly combined.
In a large bowl, whisk together 10 tablespoons vanilla Greek yogurt, 1/2 cup natural honey, 1 egg, 1 teaspoon vanilla extract, and 6 tablespoons unsweetened almond milk until smooth.
Add the dry ingredients to the wet ingredients. Fold gently until just combined, then fold in 1/2 cup mini chocolate chips (reserve a small amount of chips to sprinkle on top). Do not overmix.
In a small bowl, beat together 6 tablespoons softened reduced‑fat cream cheese and 2 tablespoons Truvia until smooth and well combined.
Spoon batter into each prepared muffin cup until about halfway full.
Use the back of the spoon to make a small depression in the center of the batter in each cup. Drop about 1/2 tablespoon of the cream cheese mixture into each depression.
Top each cream cheese mound with more batter, filling each muffin cup to about 3/4 full. Sprinkle the reserved mini chocolate chips on top of each muffin.
Bake in the preheated oven for 17 to 18 minutes, or until a toothpick inserted into the muffin portion (avoiding the cream cheese center) comes out with a few moist crumbs but no wet batter.
Let the muffins cool in the tray for 10 minutes, then transfer them to a wire rack to finish cooling.