Preheat oven to 400°F. Line a muffin pan with paper liners and set aside.
Make the cheesecake filling: In a medium bowl, beat 8 oz softened cream cheese with 1/2 cup granulated sugar until light and fluffy, about 2–3 minutes. Add 1 egg and 1/2 tsp vanilla extract and beat until smooth. Fold in 1/4 cup mini chocolate chips. Transfer the filling to a resealable (Ziploc) bag, press the filling into one corner, seal, and refrigerate until needed.
Make the dry mixture: In a large bowl, whisk together 2 cups all-purpose flour (spooned and leveled), 1/2 cup unsweetened cocoa powder, 1 tsp baking soda, and 1 tsp salt. Set aside.
Make the batter: In a medium bowl, whisk 1/2 cup coconut oil (warmed to a liquid state) with 1 cup granulated sugar until combined. Add the remaining 1 egg, 1 cup plain Greek yogurt, 1/4 cup milk, 1/4 cup cold strong coffee, and 1 tsp vanilla extract. Whisk until smooth.
Combine wet and dry: Pour the wet ingredients into the dry ingredients and stir just until combined. Stir in 1/2 cup of the 3/4 cup mini chocolate chips (reserve the remaining 1/4 cup for topping).
Transfer the muffin batter to a second resealable bag or a piping bag and press the batter into one corner. Cut off a small corner to create a spout for piping (or use a spoon).
Fill the liners: Pipe or spoon batter into each liner so that each is about halfway full, leaving a small well in the center for the filling (the batter will be thick).
Add the cheesecake filling: Remove the cheesecake filling bag from the refrigerator, snip a small corner, and pipe about 1–2 tablespoons of filling into the center of each muffin well.
Top the muffins: Add more batter on top of each filled muffin to cover the filling (about another tablespoon per muffin), then sprinkle the reserved 1/4 cup mini chocolate chips over the tops.
Bake: Place the pan in the oven and bake at 400°F for 5 minutes. Immediately reduce the oven temperature to 350°F and continue baking for an additional 12–15 minutes, or until the muffin tops spring back when lightly pressed and a toothpick inserted into the cake portion (avoiding the center filling) comes out with a few moist crumbs.
Cool: Remove the pan from the oven and let the muffins cool in the pan for 10–15 minutes. Transfer the muffins to a wire rack to cool slightly before serving.