With a burst of tangy lime and the sweet richness of blueberries, these Blueberry Lime Cheesecake Cupcakes are a vibrant twist on classic cheesecake. Perfect for summer gatherings or any day you crave a refreshing dessert, these little gems combine zesty citrus and creamy decadence in a handheld form.

The buttery vanilla base is studded with juicy blueberries, topped with a luscious lime-infused cheesecake layer, and finished off with a dazzling purple blueberry glaze. Each bite offers a satisfying balance of tart, sweet, and creamy that’s hard to resist.
What Makes Blueberry Lime Cheesecake Cupcakes So Unique?
These cupcakes stand out with their dynamic flavor pairing. Lime brings a lively acidity that brightens the creamy cheesecake base, while blueberries add natural sweetness and an eye-catching color. They’re not just cupcakes—they’re an elegant dessert experience wrapped in a cupcake liner.
Ingredients for the Blueberry Lime Cheesecake Cupcakes
- Fresh Blueberries – Essential for both the cupcake base and the topping. Their juicy texture and natural sweetness give this recipe its signature flavor.
- Lime Zest and Juice – Adds brightness and a refreshing zing that cuts through the richness of the cheesecake.
- Cream Cheese – The heart of the cheesecake layer, lending smoothness and tang.
- Sugar – Used to sweeten both the cupcake and cheesecake layers, as well as the glossy blueberry topping.
- Vanilla Extract – Enhances the overall flavor and complements the fruity elements.
- Eggs – Provide structure and help the cheesecake layer set beautifully.
- All-Purpose Flour – Gives the cupcake base its soft, tender crumb.
- Butter – Adds richness and moisture to the batter.
- Baking Powder – Helps the cupcakes rise for a fluffy texture.

How To Make the Blueberry Lime Cheesecake Cupcakes
Step 1: Prepare the Cupcake Base
Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners. In a bowl, whisk together the flour, baking powder, and a pinch of salt. In a separate bowl, cream the butter and sugar until light and fluffy. Beat in the eggs one at a time, then stir in the vanilla extract and lime zest. Gradually mix in the dry ingredients, alternating with a splash of lime juice until just combined. Fold in a handful of fresh blueberries.
Step 2: Make the Cheesecake Layer
In another bowl, beat the cream cheese with sugar until smooth. Add in an egg and a tablespoon of lime juice, mixing until creamy. Spoon this mixture on top of the cupcake batter in each liner, creating a two-layer effect.
Step 3: Bake the Cupcakes
Place the filled tin into the oven and bake for about 20-22 minutes, or until the edges are set and a toothpick inserted in the center comes out clean (some moisture from the cheesecake is okay). Allow the cupcakes to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
Step 4: Prepare the Blueberry Lime Glaze
In a small saucepan, heat a cup of blueberries with a few tablespoons of sugar and a splash of lime juice. Let it simmer until the blueberries burst and the mixture thickens slightly. For an ultra-smooth glaze, blend it and strain to remove skins. Let it cool slightly before spooning over the cooled cupcakes.
Step 5: Garnish and Serve
Top each glazed cupcake with a few whole blueberries and thin slices of candied lime or zest for a decorative finish. Chill for at least 30 minutes before serving to allow the cheesecake to firm up.
How to Serve and Store These Blueberry Lime Cheesecake Cupcakes
Serve these cupcakes slightly chilled to highlight the creamy cheesecake texture. They make a stunning dessert centerpiece for brunches, tea parties, or festive gatherings. For an elevated presentation, place them on a cake stand and garnish with extra lime zest and edible flowers.
To store, place the cupcakes in an airtight container and refrigerate for up to 4 days. If stacking, use parchment paper between layers. They also freeze beautifully—wrap each one individually in plastic wrap and store in a freezer-safe bag for up to one month. Thaw overnight in the fridge before enjoying.
Frequently Asked Questions
Can I use frozen blueberries?
Yes, frozen blueberries can be used. No need to thaw them—just fold them into the batter directly. For the glaze, cook them straight from frozen.
What if I don’t have lime?
You can substitute with lemon juice and zest for a slightly different citrus profile that still complements the blueberries well.
Can I make these cupcakes ahead of time?
Absolutely. They actually taste better the next day as the flavors meld. Prepare a day in advance and store chilled until serving.
How do I prevent the cheesecake layer from cracking?
Avoid overbaking and don’t open the oven door during baking. Letting them cool gradually also helps minimize cracks.
Is it necessary to strain the glaze?
Straining gives a smoother, more elegant finish, but it’s optional. If you prefer a rustic look, you can leave the blueberry skins in.
Can I skip the cheesecake layer?
You can, but the cheesecake layer is what makes these cupcakes extra special. If you’re short on time, consider using a simple cream cheese frosting instead.
Want More Dessert Ideas with a Fruity Twist?
If you adore these blueberry lime cheesecake cupcakes, don’t miss out on these other deliciously fruity favorites:
- Lemon Blueberry Loaf for a comforting slice with citrusy flair.
- Pineapple Coconut Dream Cake that brings tropical sweetness to your table.
- Apple Enchiladas: A Sweet and Comforting Treat for a cozy, cinnamon-spiced indulgence.
- Orange Dreamsicle Salad if you’re after a chilled, creamy citrus fix.
- Traditional German Lebkuchen when you want something spiced and festive.
Save This Pin + Share Your Results
📌 Save this recipe to your Pinterest dessert board so you can come back to it any time.
And let me know in the comments how yours turned out. Did you go extra on the lime? Add a swirl of whipped cream? Maybe swapped in lemon for a twist?
I love seeing how you all personalize these treats. Got a question or tweak? Share it below—let’s bake better together!


Irresistible Blueberry Lime Cheesecake Cupcakes
- Total Time: 47 minutes
- Yield: 12 cupcakes
Description
These cupcakes are the ultimate fusion of creamy cheesecake, zesty lime, and sweet blueberries. With a tender vanilla cake base, a smooth lime-kissed cheesecake layer, and a glossy blueberry glaze, each bite is vibrant and refreshing—perfect for any dessert table.
Ingredients
Fresh blueberries
Lime zest and juice
Cream cheese
Sugar
Vanilla extract
Eggs
All-purpose flour
Butter
Baking powder
Instructions
- Preheat oven to 350°F (175°C). Line muffin tin with cupcake liners.
- Mix dry ingredients: In a bowl, whisk flour, baking powder, and a pinch of salt.
- Cream butter and sugar: In a separate bowl, beat until fluffy. Add eggs one at a time, then mix in vanilla and lime zest.
- Combine mixtures: Alternate adding dry mix and lime juice. Fold in fresh blueberries.
- Make cheesecake layer: Beat cream cheese and sugar, then mix in an egg and lime juice.
- Layer cupcakes: Fill liners with cake batter, then top with cheesecake mixture.
- Bake for 20-22 minutes. Cool completely.
- Make glaze: Simmer blueberries, sugar, and lime juice. Blend and strain if desired.
- Glaze and garnish: Spoon glaze on cooled cupcakes. Top with blueberries and lime slices. Chill before serving.
- Prep Time: 25 minutes
- Cook Time: 22 minutes
- Category: Desserts
