Preheat oven to 350°F. Spray a 24-count mini muffin pan well with non stick cooking spray and set aside.
Add the flour, cocoa powder, baking soda, and salt to a large bowl and mix until fully combined.
In the bowl of a stand mixer fitted with the paddle attachment (or in a large mixing bowl using a hand-held mixer), beat the butter, brown sugar, and granulated sugar until light and fluffy.
Mix in the egg, vanilla, and red food coloring, making sure to mix well after each ingredient.
Slowly mix in the dry ingredients until just combined.
Scoop the dough out and evenly distribute it between all of the 24 mini muffin cavities.
Bake at 350°F for 11-13 minutes. Remove from the oven and gently press the center of each cookie in with the back of a measuring teaspoon.
Cool in the pan for 5-10 minutes, then transfer to a wire rack to finish cooling.
To make the cream cheese frosting:
In the bowl of a stand mixer fitted with the paddle attachment (or in a large mixing bowl using a hand-held mixer), beat the butter and cream cheese until smooth. Add in the powdered sugar and vanilla and mix until well combined.
Once the cookie cups have cooled completely, fill each one with frosting as desired.
Notes
Storage instructions: Since these are made with cream cheese, you'll need to store them in an airtight container in the fridge for up to 5 days.