Make the Pudding: Combine milk and instant pudding mix in a large mixing bowl. Beat with an electric mixer on medium/high for 2 minutes. Refrigerate for at least 5 minutes to thicken.
Mix Cream Cheese:Beat softened cream cheese separately on medium/high for 1 minute until fluffy. Add 1 cup of the pudding mixture and almond extract, and continue beating until smooth (about 30 seconds).
Crush the Crust:While the pudding chills, pulse chocolate graham crackers in the food processor until they're a fine crumb. Mix in some melted butter for an extra rich flavor.
Assemble the Cups:Layer the ingredients in this order: graham cracker crust, cream cheese/pudding mixture, pudding, sweet cherry, chocolate chips on the top of the cheesecake cup.
Chill:For best results, let the silky smooth chocolate cherry cheesecake chill in the fridge for at least 30 minutes. This helps the flavors merge and firms the pudding for a delicious, scoopable texture of cooled cheesecake.