Name: Irresistible Blueberry Lime Cheesecake Cupcakes
Prep time: 20 min
Cook time: 22 min
Total time: 42 min
Ingredients: 1 cup all-purpose flour; 1 tsp baking powder; 1/4 tsp salt; 1/2 cup unsalted butter (room temperature); 3/4 cup granulated sugar; 2 large eggs; 1 tsp vanilla extract; Zest of 1 lime; 8 oz full-fat cream cheese (room temperature); 2 tbsp lime juice; 1/4 cup powdered sugar (for glaze); 1/2 cup fresh or frozen blueberries (plus extra for topping); 1 tsp cornstarch; 1 tbsp water (for blueberry topping)

I’ll be honest: these Blueberry Lime Cheesecake Cupcakes have completely stolen my heart. It all started when I spotted some plump, juicy blueberries at the market and remembered the tart limes waiting in my fruit bowl. The idea to marry the richness of cheesecake with the brightness of lime and the burst of blueberries came naturally—and the result? Absolute magic.

Each bite of these cupcakes offers a creamy, tangy cheesecake center wrapped in soft vanilla cake, topped with a vivid blueberry compote and a pop of lime glaze. They’re indulgent but refreshing, rich yet zingy, and they manage to feel both homey and elegant. Whether you’re baking for a brunch, a birthday, or just a treat-yourself moment, these are the cupcakes to reach for.

Why You’ll Love This Blueberry Lime Cheesecake Cupcake Recipe

These cupcakes are not your average dessert. The cheesecake layer adds a creamy, dreamy surprise that pairs beautifully with the moist vanilla cake base. The tartness from the lime cuts through the richness and the blueberry topping adds a fruity depth that keeps every bite interesting. Visually, they’re stunning—vibrant purple glaze, fresh berries, and a hint of green lime garnish. But more importantly, they taste even better than they look.

They’re also a great make-ahead option, store beautifully, and never fail to impress at parties or afternoon tea. Once you’ve tried these, I promise you’ll find yourself making them again and again.

What Kind of Cream Cheese Should I Use?

When it comes to baking cheesecake cupcakes, the quality of cream cheese matters more than you might think. I always recommend using full-fat cream cheese (block-style, not spreadable or whipped) for the richest flavor and creamiest texture. Brands like Philadelphia tend to hold up well in baking, but any high-quality full-fat version will do the job beautifully. Avoid using low-fat or whipped cream cheese—these introduce extra moisture and air, which can ruin the structure and richness of your cheesecake layer.

Options for Substitutions

If you’re out of something or want to tweak the flavor, there’s definitely some room to play here:

Blueberries – Fresh or frozen both work. You can also swap with blackberries, raspberries, or a mix of berries.
Lime – Lemon can be used in place of lime for a citrus twist that’s equally refreshing.
Cream Cheese – For a lighter version, Neufchâtel cheese (which has less fat) can be used, but expect a slightly softer texture.
Cupcake Base – Want to make it gluten-free? Use your favorite gluten-free all-purpose baking mix.
Sweetener – Regular sugar is best, but honey or maple syrup can work in the berry topping if you’re going for a natural sweetness profile.

Just remember, any swap might slightly shift the final texture or flavor, but the essence of the cupcakes—tangy, fruity, and creamy—will still shine through.

Ingredients for These Blueberry Lime Cheesecake Cupcakes

Each ingredient in this recipe has a purpose, and together they create a layered, flavor-packed dessert that’s both luxurious and bright.

All-Purpose Flour
The backbone of the cupcake base, providing structure and a light, tender crumb.
Baking Powder
Helps the cupcakes rise just the right amount for a soft, fluffy texture.
Salt
Enhances the other flavors and balances the sweetness beautifully.
Unsalted Butter
Adds richness and moisture to the cupcake batter—room temperature is key for creaming properly.
Granulated Sugar
Sweetens the cupcakes and also helps create a light texture when beaten with the butter.
Eggs
Bind everything together and add richness; they also help the cupcakes rise and set properly.
Vanilla Extract
A must-have for depth and warmth in both the cupcake and the cheesecake layer.
Full-Fat Cream Cheese
The heart of the cheesecake center—rich, smooth, and just a little tangy.
Lime Juice and Zest
Infuses the batter and glaze with bright, citrusy zing that complements the richness of the cheesecake.
Fresh Blueberries
Sweet, juicy bursts of fruit baked into the cupcakes and piled generously on top.
Powdered Sugar
Blends into the lime glaze smoothly and adds sweetness without graininess.
Cornstarch
Used to thicken the blueberry topping and keep it glossy and neat.
Milk (or Cream)
Helps smooth out the glaze or batter if needed—adds a hint of richness and softness.

Step 1: Prepare the Cupcake Base

Preheat your oven to 350°F (175°C) and line a cupcake pan with paper liners. In a medium bowl, whisk together flour, baking powder, and salt. In a separate large bowl, cream the softened butter and granulated sugar until light and fluffy. Add in the eggs one at a time, beating well after each addition. Mix in the vanilla extract and lime zest.

Step 2: Make the Cheesecake Filling

In a bowl, beat the full-fat cream cheese until smooth. Add in sugar, a splash of vanilla extract, and lime juice. Mix until creamy and fully incorporated. You want a silky, spoonable texture—this will form the luscious core inside your cupcakes.

Step 3: Assemble the Cupcakes

Spoon about one tablespoon of cupcake batter into each liner. Add a teaspoon of the cheesecake filling on top, then cover with another spoonful of batter. Drop in a few fresh blueberries before baking. The berries will sink slightly and burst with flavor in the oven.

Step 4: Bake

Place the filled cupcake pan into the preheated oven and bake for 20–22 minutes, or until the tops are golden and a toothpick inserted into the cake part comes out clean (don’t poke the cheesecake center). Let them cool completely on a wire rack.

Step 5: Make the Blueberry Topping

In a small saucepan, heat fresh blueberries with a spoonful of sugar and a splash of water. Stir in a bit of cornstarch to thicken and simmer until the berries break down slightly and the mixture becomes glossy. Let it cool before topping.

Step 6: Make the Lime Glaze

Whisk powdered sugar with fresh lime juice until smooth and pourable. You can adjust the consistency with more sugar or juice. This glaze ties everything together with a tangy finish.

Step 7: Decorate

Once cupcakes are cooled, spoon the blueberry topping generously over each one. Drizzle with the lime glaze and top with a small slice of candied lime or an extra blueberry for garnish. The colors pop, and the flavors burst even more.

How Long to Cook the Blueberry Lime Cheesecake Cupcakes

These cupcakes take 20 to 22 minutes in a preheated 350°F (175°C) oven. You’ll know they’re ready when the cake portion springs back gently to the touch and the edges look lightly golden. Because of the cheesecake center, avoid overbaking—check a bit early, especially if your oven runs hot.

Let them cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. The cheesecake layer sets as they cool, so resist the urge to bite into one too soon!

Tips for Perfect Blueberry Lime Cheesecake Cupcakes

Use Room Temperature Ingredients
This includes butter, eggs, and cream cheese. It makes the batter smoother and helps everything blend evenly.
Don’t Overmix the Batter
Overmixing can make your cupcakes dense. Mix just until the ingredients are combined.
Fresh Lime Zest is Gold
It adds a bright, floral zing that bottled juice just can’t replicate. Use a microplane and only zest the green layer—not the bitter white pith.
Layer Carefully
Spoon the cheesecake filling gently into the center to keep the layers distinct. A small cookie scoop works perfectly for this.
Let Toppings Cool
Warm glaze or blueberry compote can slide off the cupcakes. Let them cool before decorating for a clean finish.
Chill Before Serving (Optional)
For a firmer cheesecake center and a refreshing twist, refrigerate the cupcakes for an hour before serving. The contrast of cool creaminess and zesty lime is divine.

Watch Out for These Mistakes While Cooking

Even the best bakers can hit a snag, so here are some common pitfalls to avoid:

Overfilling the Liners
With cheesecake and batter layers, the liners should be filled only about 3/4 full to prevent overflow.
Undercooking the Cupcakes
The cheesecake center may stay soft, but the cupcake edges should be golden. Don’t mistake the soft center for being raw—check the cake part for doneness instead.
Using Cold Cream Cheese
This leads to a lumpy filling. Let it come to room temperature before beating to ensure a smooth texture.
Skipping the Cooling Time
These cupcakes firm up as they cool. If you decorate or serve them too soon, you’ll miss out on that creamy cheesecake consistency.
Storing While Warm
Putting warm cupcakes into the fridge or container will trap steam, making them soggy. Always let them cool completely.

What to Serve With Blueberry Lime Cheesecake Cupcakes?

These cupcakes are excellent on their own, but they shine even brighter when served with the right companions.

Sparkling Limeade

The citrus echoes the lime in the cupcakes and adds a refreshing, fizzy contrast.

Vanilla Bean Ice Cream

Soft, cool, and subtly sweet—it melts beautifully next to the tangy cupcake.

Fresh Berry Salad

A light side dish with strawberries, blackberries, and mint balances out the richness.

Whipped Cream with Lime Zest

A fluffy, airy swirl on the side (or piped on top!) brings a delicate creaminess.

Espresso or Cold Brew

Bold coffee balances the sweetness and lifts the citrus notes even more.

Coconut Chips

Serve them scattered on the plate for a tropical crunch.

Shortbread Cookies

Buttery and simple, they complement the cupcake’s complexity without stealing the show.

Storage Instructions

These Blueberry Lime Cheesecake Cupcakes store beautifully, making them a great make-ahead treat.

Refrigerator: Store in an airtight container in the fridge for up to 5 days. The cheesecake center keeps well, and the flavors deepen slightly over time.
Freezer: You can freeze the undecorated cupcakes (without glaze or topping) for up to 2 months. Wrap each one tightly in plastic wrap and place them in a zip-top bag. Thaw overnight in the fridge, then add the blueberry compote and lime glaze just before serving.
Make-Ahead Tips: You can bake the cupcakes a day ahead and refrigerate them, then add the toppings on the day of serving for the freshest presentation.

Estimated Nutrition

Here’s a rough estimate per cupcake (based on a standard batch of 12), including both the cheesecake filling and toppings:

Calories: ~280 kcal
Total Fat: ~15g
Saturated Fat: ~9g
Carbohydrates: ~32g
Sugar: ~22g
Protein: ~4g
Fiber: ~1g
Cholesterol: ~60mg
Sodium: ~120mg

Keep in mind these values can vary based on your exact ingredients, portion size, and how generous you are with the blueberry and glaze toppings.

Frequently Asked Questions

Can I use frozen blueberries instead of fresh?

Yes! Frozen blueberries work just fine for both the cupcake batter and the topping. No need to thaw them—just toss them in frozen to avoid discoloring the batter.

Can I make these cupcakes ahead of time?

Absolutely. Bake them the day before and store in the fridge. Add the blueberry topping and lime glaze right before serving for best results.

How do I know when the cupcakes are done?

The edges of the cupcake should be golden, and the top should spring back gently when pressed. Don’t rely on a toothpick test through the cheesecake center—it’ll always come out soft.

Can I make this recipe gluten-free?

Yes, substitute a good-quality 1:1 gluten-free all-purpose flour blend. The texture may vary slightly, but the flavor will still shine.

Do I need to use paper liners?

Liners are highly recommended for easy removal and cleaner presentation. If you skip them, be sure to grease the pan thoroughly and expect a slightly crispier edge.

Can I double the recipe?

Definitely. Just make sure not to crowd your oven so the heat distributes evenly. You may need to rotate your pans halfway through baking.

Can I turn this into a full cake?

Yes! Pour the batter and cheesecake filling into an 8-inch round pan (springform if possible). Increase baking time to around 45–50 minutes and check for doneness.

How should I decorate them for a party?

Add a swirl of whipped cream, a fresh blueberry, and a pinch of lime zest on top for a polished, bakery-style look. Edible flowers or candied lime slices also make for an elegant finish.

Conclusion

Blueberry Lime Cheesecake Cupcakes are the kind of dessert that bring a little joy to any occasion. From their hidden creamy centers to the zippy lime glaze and vibrant blueberry topping, they’re full of surprise, texture, and flavor. I’ve made these for birthdays, showers, and just because—and every time, they disappear fast. They’re playful, elegant, and totally unforgettable.

Give them a try, and I think you’ll see why this recipe has a permanent place in my dessert rotation.