
This tangy lime and sweet blueberry combination creates the most irresistible handheld cheesecakes you will ever try. The graham cracker crust provides the perfect buttery base while the creamy filling balances tartness and sweetness in every bite. These cupcakes have become my summer entertaining staple whenever I need an impressive yet easy dessert.
I first made these cupcakes for a garden party last summer and they disappeared within minutes. Now they're requested at every family gathering from Memorial Day through Labor Day, especially by my lime loving sister in law.
Ingredients
- Graham cracker crumbs: creates a traditional cheesecake base with the perfect texture and flavor
- Sugar: balances the tartness of the lime and adds sweetness to the crust
- Unsalted butter: binds the crust and adds richness, always use unsalted to control salt content
- Cream cheese: forms the creamy base, Philadelphia brand works best for smooth texture
- Large eggs: provide structure and richness to the filling
- Lime juice: adds brightness, always use fresh squeezed for the best flavor
- Lime zest: intensifies the citrus flavor without adding more liquid
- Blueberries: offer bursts of sweetness and color, choose plump firm berries
- Whipped cream: lightens the dessert and adds a decorative touch
- Extra blueberries for garnish: make the presentation pop with color
Step-by-Step Instructions
- Prepare the Oven and Pan:
- Preheat your oven to exactly 325°F for gentle even baking. Line a standard cupcake pan with paper liners making sure they sit properly in each cavity. The lower temperature is crucial for preventing cracks in your cheesecakes.
- Create the Perfect Crust:
- Mix graham cracker crumbs, sugar, and melted butter until the mixture resembles wet sand. Press about 1 tablespoon firmly into each liner using the bottom of a small glass or measuring cup. The pressure creates a solid base that wont crumble when serving.
- Make the Cream Cheese Filling:
- Beat room temperature cream cheese and sugar for at least 3 minutes until completely smooth with no lumps whatsoever. Add eggs one at a time, mixing just until incorporated. Overmixing can incorporate too much air causing cracks. Add lime juice and zest, mixing gently for even distribution of flavor.
- Add the Blueberries:
- Fold blueberries into the batter using a rubber spatula with a gentle turning motion. This preserves the berries integrity while distributing them throughout the batter. If using frozen berries, keep them frozen to prevent color bleeding.
- Fill the Liners:
- Spoon the cheesecake mixture carefully into each prepared liner to about three quarters full. The batter will rise slightly during baking then settle as it cools. Tap the pan gently on the counter to release any air bubbles.
- Bake to Perfection:
- Bake for 20 to 25 minutes until the centers are just set but still slightly jiggly. The cheesecakes will continue cooking from residual heat after removal from the oven. Overbaking causes dry texture and cracks.
- Cool Properly:
- Allow the cupcakes to cool completely in the pan placed on a wire rack. Once at room temperature, refrigerate for at least 2 hours or preferably overnight. This cooling process is essential for the perfect texture.
- Garnish Before Serving:
- Top with freshly whipped cream and additional blueberries just before serving for the most attractive presentation. A small lime zest curl makes an impressive finishing touch.

These cupcakes remind me of summers at my grandmothers lake house where we would pick wild blueberries every morning. The combination of lime and blueberry always takes me back to those carefree days of bare feet and sticky fingers from berry picking.
Perfect Storage
These cheesecake cupcakes actually improve with time as the flavors meld together in the refrigerator. Store them in an airtight container for up to 5 days, keeping the whipped cream and fresh blueberry garnish separate until serving time. The cupcakes can also be frozen without the toppings for up to 3 months. Wrap each one individually in plastic wrap then place in a freezer bag. Thaw overnight in the refrigerator before garnishing and serving.
Smart Substitutions
For a gluten free version, substitute the graham cracker crumbs with gluten free cookies or a mixture of almond flour and melted butter. Lemon can replace lime for a slightly different flavor profile that works equally well with blueberries. For a lighter version, use Neufchâtel cheese instead of full fat cream cheese and reduce the sugar by 2 tablespoons. Greek yogurt can be substituted for the whipped cream topping for added protein and tanginess.
Seasonal Variations
While blueberries shine in this recipe, you can create seasonal variations throughout the year. Try strawberries in spring, raspberries in early summer, blackberries in late summer, or even cranberries in winter. Each berry brings its own character while maintaining the delightful contrast with the citrus. For fall gatherings, consider adding a pinch of cinnamon to the crust and replacing the berries with diced apples sautéed with a touch of brown sugar.
Serving Ideas
These versatile treats can be dressed up or down depending on the occasion. For casual gatherings, serve them straight from the refrigerator on a simple platter. For more formal events, place each cupcake on a small dessert plate with a drizzle of blueberry coulis, a sprig of mint, and a decorative lime twist. They pair beautifully with coffee, tea, or even a dessert wine like Moscato. For brunch, serve alongside a mimosa with a splash of lime juice instead of the traditional orange.

Frequently Asked Questions About the Recipe
- → Can I use frozen blueberries instead of fresh?
Yes, you can use frozen blueberries, but make sure to thaw and drain them thoroughly before folding into the batter to prevent excess moisture from affecting the texture of your cheesecake cupcakes.
- → How long do these cheesecake cupcakes stay fresh?
These cupcakes will stay fresh for up to 3-4 days when stored in an airtight container in the refrigerator. For best flavor and texture, add the whipped cream and blueberry garnish just before serving.
- → Can I freeze these cheesecake cupcakes?
Yes, these cupcakes freeze well for up to 2 months. Freeze them without the whipped cream topping, wrapped individually in plastic wrap and stored in an airtight container. Thaw overnight in the refrigerator and add fresh toppings before serving.
- → What can I substitute for graham cracker crumbs?
If graham crackers aren't available, you can substitute with digestive biscuits, vanilla wafers, or any plain sweet cookie crumbs. Just process them to fine crumbs and use the same measurement as called for in the recipe.
- → How do I know when the cheesecake cupcakes are done baking?
The cupcakes are done when the centers are mostly set but still have a slight jiggle. They'll continue to firm up as they cool. Avoid overbaking, which can cause cracks and a dry texture. The edges should be firm, and the center should be just set, similar to a traditional cheesecake.
- → Can I make these without the lime flavor?
Absolutely. You can omit the lime juice and zest for a pure blueberry cheesecake, or substitute with lemon for a different citrus pairing. If removing the citrus entirely, consider adding 1 teaspoon of vanilla extract to enhance the flavor.