Preheat your oven to 350°F (175°C) to ensure even baking.
Line a muffin tin with paper liners or grease it lightly with coconut oil.
In a medium bowl, beat together the cream cheese, 1/2 cup granulated sugar, 1 egg, and 1/2 tsp vanilla extract until smooth. Stir in 1/4 cup mini chocolate chips and set aside.
In a large bowl, whisk together flour, cocoa powder, baking soda, and salt.
In another bowl, whisk together warm coconut oil, 1 cup granulated sugar, 1 egg, Greek yogurt, milk, cold coffee, and 1 tsp vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and mix gently until just combined.
Scoop muffin batter into each cup, filling halfway. Add cheesecake filling on top, then cover with more batter until 3/4 full.
Sprinkle remaining 3/4 cup mini chocolate chips on top.
Bake for 20-25 minutes, or until a toothpick comes out clean.
Let cool in the pan for 5 minutes before transferring to a cooling rack.