In a large bowl, whisk together flour, cocoa powder, baking soda and salt. Set aside.
In a medium bowl, whisk together coconut oil and sugar.
Add the egg, Greek yogurt, milk, coffee and vanilla extract and continue whisking until combined.
Stir wet ingredients into dry ingredients just until combined. Stir in 1/2 a cup of mini chocolate chips.
Transfer muffin batter to a ziploc bag and cut off one corner.
Pipe batter into each liner until about halfway full leaving the center empty if possible. The batter is very thick.
Remove the cheesecake filing from the refrigerator and snip one corner of the ziploc bag. Press the tip of the bag into the center of each muffin and squeeze about two tablespoons of filling into the center of each muffin.
Top with another tablespoon of muffin batter and sprinkle with mini chocolate chips.
Bake at 400F for 5 minutes. Turn temperature down to 350F and continue baking for an additional 12 to 15 minutes or until the top of the muffins springs back when pressed.
Let cool slightly before serving.