In a medium bowl, beat together the softened cream cheese and 1/2 cup granulated sugar using an electric mixer until smooth and creamy. Add 1 egg and 1/2 tsp vanilla extract, mixing until well combined. Gently fold in 1/4 cup mini chocolate chips. Set aside.
Preheat your oven to 350°F (175°C). Grease your muffin tin or line it with muffin liners to prevent sticking.
In a large bowl, whisk together 2 cups all-purpose flour, 1/2 cup unsweetened cocoa powder, 1 tsp baking soda, and 1 tsp salt.
In another bowl, whisk together 1/2 cup melted coconut oil, 1 cup granulated sugar, 1 egg, 1 cup plain Greek yogurt, 1/4 cup milk, 1/4 cup cold strong coffee, and 1 tsp vanilla extract until smooth.
Gradually add the wet mixture to the dry ingredients, stirring until just combined.
Spoon about 2 tablespoons of muffin batter into each muffin cup. Then, add a generous tablespoon of the cream cheese filling on top of the batter. Finally, cover the cream cheese filling with another tablespoon of muffin batter.
Sprinkle the remaining 1/2 cup of mini chocolate chips on top of each muffin.
Bake in the preheated oven for 18-20 minutes or until a toothpick inserted into the muffin comes out clean. Allow the muffins to cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely.