Line a 12-cup muffin pan with liners and preheat the oven to 400°F (200°C).
Make the cheesecake filling: In a medium bowl, beat 8 oz softened cream cheese and 1/2 cup granulated sugar until light and fluffy, about 2–3 minutes. Add 1 room-temperature egg and 1/2 tsp vanilla extract and beat until smooth. Stir in 1/4 cup mini chocolate chips. Transfer the filling to a zip-top bag, seal, and refrigerate until firm enough to pipe (at least 30 minutes).
Whisk the dry ingredients: 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 muffin batter: In a medium bowl, whisk 1/2 cup liquid coconut oil and 1 cup granulated sugar until combined. Whisk in 1 room-temperature egg. Add 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 mixture into the dry ingredients and stir gently just until combined—do not overmix. Fold in 1/2 cup of the 3/4 cup mini chocolate chips (reserve the remaining 1/4 cup for topping).
Transfer the batter to a piping bag or a zip-top bag with one corner snipped, or use a spoon for filling the liners. The batter will be thick.
Pipe or spoon batter into each prepared liner to fill about halfway, leaving a visible cavity in the center for the cheesecake filling.
Remove the chilled cheesecake filling bag from the refrigerator, snip a small corner, and pipe about 2 tablespoons of filling into the center of each muffin, keeping the filling centered.
Top each filled muffin with roughly 1 tablespoon of the remaining muffin batter (enough to mostly cover the filling) and sprinkle the tops with the remaining 1/4 cup mini chocolate chips.
Bake in the preheated oven at 400°F for 5 minutes. Without opening the oven, reduce the oven temperature to 350°F and bake for an additional 12–15 minutes, or until the muffin tops spring back when gently pressed and a toothpick inserted into the cake portion (avoiding the center filling) comes out with a few moist crumbs.
Remove the pan from the oven and let the muffins cool in the pan for 5–10 minutes, then transfer to a wire rack to cool slightly before serving.