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.
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).
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.
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.
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.