Step 1: Prepare the Cream Cheese Filling. In a medium bowl, beat together the softened cream cheese, ½ cup granulated sugar, 1 egg, ½ tsp vanilla extract, and ¼ cup mini chocolate chips until smooth and creamy. Set aside.
Step 2: Preheat Your Oven. Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.
Step 3: Mix the Dry Ingredients. In a large bowl, whisk together 2 cups all-purpose flour, ½ cup unsweetened cocoa powder, 1 tsp baking soda, and 1 tsp salt until well combined.
Step 4: Combine the Wet Ingredients. In another bowl, combine ½ cup melted coconut oil, 1 cup granulated sugar, 1 large egg, 1 cup plain Greek yogurt, ¼ cup milk, ¼ cup cold strong coffee, and 1 tsp vanilla extract. Whisk until smooth.
Step 5: Combine Wet and Dry Ingredients. Gradually add the wet mixture to the dry ingredients, stirring gently until just combined.
Step 6: Fold in Chocolate Chips. Gently fold in ¾ cup of mini chocolate chips into the muffin batter.
Step 7: Fill the Muffin Tin. Spoon a dollop of muffin batter into each muffin cup, filling them about halfway. Then, add a spoonful of the cream cheese mixture on top, followed by more muffin batter to cover.
Step 8: Bake. Bake in the preheated oven for 18-20 minutes, or until a toothpick comes out clean.
Step 9: Cool. Let the muffins cool in the pan for about 5 minutes before transferring to a cooling rack.