
This blackberry lime cheesecake cupcake recipe combines the perfect balance of tangy lime and sweet blackberries in a creamy cheesecake base. The graham cracker crust provides a delightful crunch that complements the smooth filling, making these cupcakes an impressive dessert for any occasion.
I first made these cupcakes for my sister's bridal shower and they were such a hit that they've become my signature dessert for gatherings. The contrast between the purple blackberries and green lime zest never fails to impress guests.
Ingredients
- Graham cracker crumbs: Create the perfect buttery base for these cheesecake cupcakes
- Cream cheese: Must be fully softened to room temperature for the smoothest texture
- Fresh lime juice: Adds brightness that bottled juice simply cannot match
- Blackberry jam: Creates a beautiful swirl and concentrated flavor throughout
- Fresh blackberries: Provide bursts of juicy flavor and stunning visual appeal
- Heavy cream: Whipped to stiff peaks creates a light cloud-like topping
- Lime zest: Brings color and concentrated citrus aroma to finish the cupcakes
Step-by-Step Instructions
- Prepare the crust:
- Mix graham cracker crumbs with melted butter until the mixture resembles wet sand. Press about one tablespoon firmly into each cupcake liner using the back of a measuring spoon to create an even layer. The crust should be compact to prevent crumbling when serving.
- Create the filling:
- Beat softened cream cheese and sugar until completely smooth and no lumps remain about 2-3 minutes. Add eggs one at a time allowing each to fully incorporate before adding the next. This method prevents air bubbles from forming in your batter. Stir in vanilla extract and fresh lime juice until just combined being careful not to overmix.
- Assemble the cupcakes:
- Spoon a tablespoon of blackberry jam onto each crust spreading it slightly but not all the way to the edges. Pour the cream cheese mixture over the jam filling each liner about three-quarters full. The batter will rise slightly during baking.
- Bake to perfection:
- Place the cupcakes in a preheated oven and bake for 20-25 minutes until the centers are just set but still slightly jiggly. The tops should not brown significantly. Remove from oven and allow to cool completely at room temperature before chilling.
- Finish with toppings:
- Whip heavy cream to stiff peaks using chilled beaters and bowl for best results. Dollop or pipe the cream onto each cooled cupcake. Arrange fresh blackberries on top and sprinkle with lime zest just before serving for maximum visual impact.

The secret to these cupcakes is in the balance of flavors. I discovered that adding the lime juice directly to the cream cheese mixture rather than as a separate layer creates a more harmonious flavor profile. My family particularly loves the hidden jam layer that creates a wonderful surprise with each bite.
Storage Tips
These cheesecake cupcakes can be stored in an airtight container in the refrigerator for up to 3 days. For the best presentation wait to add the fresh berries and lime zest until just before serving. The whipped cream topping will hold its shape nicely in the refrigerator thanks to the stabilizing effect of being placed on the dense cheesecake base.
Make Ahead Options
You can prepare these cupcakes completely up to 48 hours in advance making them perfect for entertaining. The flavors actually develop and improve with time as the lime and blackberry notes meld together. If freezing wrap individual unfrosted cupcakes tightly in plastic wrap then foil and freeze for up to one month. Thaw overnight in the refrigerator before topping and serving.
Flavor Variations
The blackberry lime combination is divine but this versatile recipe works wonderfully with other fruit pairings. Try raspberry lemon for a classic combination or blueberry orange for something unexpected. You can also add a tablespoon of liqueur that complements your fruit choice to the cream cheese mixture for an adult version perfect for dinner parties.

Frequently Asked Questions About the Recipe
- → Can I make these cheesecake cupcakes ahead of time?
Yes! These cupcakes are actually perfect for making ahead. They can be prepared up to 2 days in advance and kept refrigerated. Just add the whipped cream topping and garnishes shortly before serving for the best presentation and texture.
- → How do I know when the cheesecake cupcakes are properly baked?
The cupcakes are done when the centers are just set but still have a slight jiggle. They should not be completely firm when you remove them from the oven as they will continue to set while cooling. Overbaking can cause cracks and a dry texture.
- → Can I freeze these blackberry lime cheesecake cupcakes?
Yes, you can freeze them for up to 1 month. Freeze them without the whipped cream topping and garnishes. Wrap each cooled cupcake individually in plastic wrap, then place in a freezer-safe container. Thaw overnight in the refrigerator and add fresh toppings before serving.
- → What can I use instead of graham crackers for the crust?
Digestive biscuits make an excellent substitute for graham crackers. You could also use shortbread cookies, vanilla wafers, or gingersnaps for a different flavor profile. For a more tropical twist, try using crushed lime cookies to enhance the lime flavor.
- → Can I use frozen blackberries instead of fresh?
Yes, frozen blackberries can work for the jam component. Thaw and drain them well before using to avoid excess moisture. For the garnish, fresh berries are recommended for the best appearance and texture, but in a pinch, thawed frozen berries can work too.
- → How do I prevent my cheesecake cupcakes from cracking?
To prevent cracks, avoid overmixing the batter which incorporates too much air. Bake at a moderate temperature (325°F is perfect) and don't overbake. Some bakers also recommend placing a shallow pan of water on the rack below the cupcakes to create moisture in the oven.