Preheat the oven to 325 degrees F (160 degrees C). Line muffin cups with paper or foil liners.

Remove top from each sandwich cookie; crush tops and set aside. Place creme-topped cookies in the prepared muffin cups, creme-side up.

Beat cream cheese, sugar, cocoa, and vanilla in a large bowl with an electric mixer until fluffy. Mix in eggs until blended. Fill the prepared muffin cups 3/4 full; sprinkle 1/4 cup reserved cookie crumbs on top. Discard remaining crumbs or save for another use.

Bake in the preheated oven until set, 20 to 25 minutes. Cool completely; cover and refrigerate for at least 2 hours.

Top each cheesecake with 2 tablespoons cherry filling and a dollop of whipped topping just before serving.