If you are a fan of tangy, creamy desserts with a delightful crunch and a cloud-like finish, this Lemon Meringue Cheesecake Cupcakes Recipe will quickly become one of your all-time favorites. Combining the zestiness of lemon with the rich smoothness of cheesecake and topped with a perfectly toasted meringue, each bite is an irresistible balance of sweetness and tartness. These individual-sized treats are not only charming to look at but also bring together classic flavors in an exciting and approachable way that’s great for sharing or enjoying solo.

Ingredients You’ll Need
Gathering simple yet essential ingredients is the first step to creating your delicious Lemon Meringue Cheesecake Cupcakes Recipe. Each component plays a unique role in delivering the right texture, flavor, and color for these irresistible cupcakes.
- 90g crushed graham crackers (3/4 cup): This makes a buttery, crunchy crust that forms the perfect base and adds texture contrast.
- 1/4 teaspoon flaky kosher salt: Enhances flavors by balancing the sweetness.
- 40g melted, unsalted butter (3 tablespoons): Binds the graham cracker crust and enriches the flavor.
- 350g softened cream cheese (12 ounces): The creamy heart of the cheesecake that gives it luscious smoothness.
- 100g white sugar (1/2 cup): Sweetens the cheesecake with a clean, classic taste.
- 1 tablespoon plain flour: Adds just enough structure to keep the cheesecake firm but tender.
- 60g sour cream (1/4 cup): Provides a subtle tang and balances the richness beautifully.
- 1 teaspoon pure vanilla extract: Deepens the overall flavor with warm, comforting notes.
- 60ml fresh lemon juice (1/4 cup): Brings refreshing citrus brightness and acidity.
- Lemon zest from one fruit: Adds vibrant aroma and extra lemon flavor in every bite.
- 2 big eggs: Helps set the cheesecake filling while maintaining creaminess.
- 3 large whites from eggs: The foundation of the fluffy meringue topping.
- 150g granulated sugar (3/4 cup): Sweetens the meringue and stabilizes it for that glossy finish.
- 1/4 teaspoon tartar powder for stability: Ensures your meringue maintains its structure.
- A small pinch of kosher salt: Balances the sweetness in the meringue for perfect taste.
How to Make Lemon Meringue Cheesecake Cupcakes Recipe
Step 1: Prepare the Crust
Start by preheating your oven to 160°C (320°F) and lining a 12-cup muffin pan with cupcake liners. Mix the crushed graham crackers, melted butter, and a pinch of kosher salt until well combined. Press this mixture firmly into the bottoms of each liner to create a sturdy, flavorful base. Bake for 5 minutes to set the crust and then let it cool completely, setting the stage for a crisp, buttery texture underneath the creamy filling.
Step 2: Make the Cheesecake Batter
Using a mixer, beat the softened cream cheese until it’s smooth and creamy. Incorporate the sugar and lemon zest; this combination ensures a good balance of tart and sweet flavors. Add the flour and continue mixing until the batter is light and fluffy, which makes the final cupcakes delightfully airy and tender.
Step 3: Add Sour Cream, Vanilla, and Lemon Juice
Blend in sour cream, vanilla extract, and fresh lemon juice carefully but thoroughly. These ingredients enhance the cheesecake’s tanginess while giving it a luscious texture that’s not too heavy. Proper mixing here ensures even flavor distribution throughout the cupcakes.
Step 4: Incorporate Eggs
Add the eggs one at a time, beating just enough to combine. This gentle mixing is crucial—it prevents overworking the batter, which can lead to cracks or a dense texture. The eggs act as a binding agent, giving the cheesecake structure and that melt-in-your-mouth richness.
Step 5: Bake the Cheesecake Cupcakes
Pour the batter evenly over the cooled crusts in your muffin liners. Bake at 160°C (320°F) for 18-20 minutes. You’ll know they’re done when the centers still have a slight wiggle; this means your cupcakes will be decadently creamy once chilled rather than dry and crumbly.
Step 6: Chill Thoroughly
Let your cupcakes cool completely at room temperature, then refrigerate them for about 3 hours. This step is key to letting the cheesecake set perfectly, intensifying flavors, and preparing the surface for the meringue topping.
Step 7: Make the Meringue
Combine the egg whites, granulated sugar, salt, and cream of tartar in a heatproof bowl placed over simmering water. Whisk constantly until the sugar dissolves and the mixture reaches 71°C (160°F). This gentle heating makes the meringue safe to eat and sets the stage for that stunning glossy finish.
Step 8: Whip to Glossy Peaks
Transfer the warm mixture to a mixer and whip on high for 5-8 minutes, until you see stiff, glossy peaks that hold their shape beautifully. This is the magical fluffy cloud that will crown your lemon meringue cheesecake cupcakes, giving them that classic visual and textural charm.
Step 9: Top and Toast the Meringue
Generously spread or pipe the meringue over the chilled cheesecake cupcakes. For that showroom finish, use a kitchen torch to lightly brown the meringue until it has a delicate toasted color. This step isn’t just for looks—the toasty flavor adds a lovely depth and contrast to the bright citrus and creamy cheesecake below.
How to Serve Lemon Meringue Cheesecake Cupcakes Recipe

Garnishes
To elevate the presentation and add an extra layer of flavor, consider garnishing with a few curls of lemon zest or a thin slice of fresh lemon. A sprinkle of finely chopped fresh mint can add a refreshing color contrast and a hint of herbal brightness that complements the lemon beautifully.
Side Dishes
These cupcakes shine as a dessert on their own, but pairing them with lightly sweetened whipped cream or a scoop of vanilla bean ice cream takes the experience to another level. Fresh berries, such as raspberries or blueberries, also make a lovely, colorful accompaniment that balances the tang.
Creative Ways to Present
Place your Lemon Meringue Cheesecake Cupcakes Recipe on a rustic wooden board or a chic cake stand for an eye-catching display. Try piping the meringue in different shapes or adding edible flowers for a special occasion. Offering them in pretty cupcake wrappers or small dessert plates makes them perfect for parties or intimate gatherings alike.
Make Ahead and Storage
Storing Leftovers
After serving, keep any leftover Lemon Meringue Cheesecake Cupcakes Recipe refrigerated in an airtight container to maintain freshness and prevent the meringue from weeping or becoming sticky. They will stay delicious for up to 3 days when properly stored.
Freezing
If you want to make these cupcakes in advance, freeze them before adding the meringue topping. Wrap each cheesecake cupcake tightly in plastic wrap and then place them in a freezer-safe container. When you’re ready to serve, thaw them overnight in the fridge and prepare the meringue fresh for best results.
Reheating
Because these cheesecakes are best enjoyed chilled, avoid reheating. Instead, let frozen cupcakes thaw slowly in the refrigerator. If you toasted the meringue before freezing, you can refresh the golden finish with a quick touch of the torch before serving for that fresh-baked feel.
FAQs
Can I use regular sugar instead of granulated sugar for the meringue?
Granulated sugar is preferred because it dissolves evenly when heated, creating a smooth, glossy meringue. Powdered sugar contains cornstarch which can affect the texture, so it’s best to stick with granulated sugar for the meringue topping.
What if I don’t have a kitchen torch to brown the meringue?
You can carefully place the cupcakes under a broiler for a minute or two, watching closely to avoid burning. Keep the oven door slightly open to monitor the color change. Alternatively, serving the meringue without toasting is perfectly delicious too!
Can I substitute the lemon juice with lime juice?
Yes! Lime juice works as a great substitute and will give your Lemon Meringue Cheesecake Cupcakes Recipe a fresh twist. The flavor will be slightly different but still wonderfully tangy and refreshing.
Why do the cupcakes need sour cream in the batter?
Sour cream adds moisture and a subtle tang that balances the richness of the cream cheese. It also contributes to a smooth texture without weighing the batter down, making the cupcakes delightfully creamy.
How important is using fresh lemon juice and zest?
Fresh lemon juice and zest dramatically elevate the flavor profile of these cupcakes. Bottled juice lacks the brightness and nuance that fresh lemons bring. The zest oil contains aromatic compounds that provide a vibrant lemon essence, making the difference truly noticeable.
Final Thoughts
There’s something truly magical about this Lemon Meringue Cheesecake Cupcakes Recipe that just brings joy to any occasion. From the crisp graham cracker crust to the luscious lemon-infused cheesecake and the fluffy, toasted meringue topping, every bite feels like a fresh celebration of flavor and texture. Trust me, once you try making these cupcakes, they’ll be a delightful staple in your dessert repertoire — perfect for impressing guests or treating yourself to a scrumptiously bright and creamy indulgence.
Print
Lemon Meringue Cheesecake Cupcakes Recipe
- Prep Time: 30 minutes
- Cook Time: 25 minutes
- Total Time: 3 hours 30 minutes
- Yield: 12 servings
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
Delight in these individual Lemon Meringue Cheesecakes featuring a buttery graham cracker crust, a tangy lemon-infused creamy cheesecake filling, and a delicate toasted meringue topping. Perfectly portioned in a 12-cup muffin pan, these cheesecakes offer a luscious blend of sweet and tart flavors finished with a beautiful golden meringue layer.
Ingredients
Crust
- 90g crushed graham crackers (3/4 cup)
- 1/4 teaspoon flaky kosher salt
- 40g melted, unsalted butter (3 tablespoons)
Cheesecake Filling
- 350g softened cream cheese (12 ounces)
- 100g white sugar (1/2 cup)
- 1 tablespoon plain flour
- 60g sour cream (1/4 cup)
- 1 teaspoon pure vanilla extract
- 60ml fresh lemon juice (1/4 cup)
- Lemon zest from one fruit
- 2 large eggs
Meringue Topping
- 3 large egg whites
- 150g granulated sugar (3/4 cup)
- 1/4 teaspoon tartar powder for stability
- A small pinch of kosher salt
Instructions
- Preheat and prepare pan: Set the oven to 160°C (320°F) and place liners into a 12-cup muffin pan to prepare for baking.
- Make the crust: Combine melted butter, crushed graham crackers, and a pinch of salt in a bowl. Press this mixture evenly into the bottom of each liner in the muffin pan. Bake for 5 minutes, then set aside to cool.
- Blend cream cheese: Beat the softened cream cheese until smooth and creamy. Mix the sugar with lemon zest and add this to the cream cheese along with the flour, whipping until the mixture becomes light and fluffy.
- Add wet ingredients: Stir in the sour cream, vanilla extract, and fresh lemon juice thoroughly to combine the mixture evenly.
- Incorporate eggs: Add the two large eggs one at a time, beating lightly after each addition just enough to blend fully without overmixing.
- Fill and bake: Spoon the cheesecake batter evenly into the prepared liners over the crust. Bake for 18-20 minutes until the centers jiggle slightly when nudged.
- Cool and chill: Allow the cheesecakes to cool completely at room temperature before transferring them to the refrigerator for at least 3 hours to set.
- Prepare meringue mixture: In a heatproof bowl placed over simmering water, combine the egg whites, granulated sugar, kosher salt, and cream of tartar.
- Heat meringue: Whisk continuously until the mixture reaches 71°C (160°F), about 5-10 minutes. This step ensures the sugar dissolves and the egg whites are safe to eat.
- Whip meringue: Remove from heat and whip the mixture with an electric mixer until glossy peaks that hold their shape form, which should take another 5-8 minutes.
- Top cheesecakes: Spread or pipe the prepared meringue on top of the chilled cheesecakes evenly.
- Toast meringue: Use a culinary torch to lightly brown the meringue surface to add a toasty finish and enhance the flavor.
Notes
- Ensure cream cheese is softened to room temperature for a smooth filling.
- Be careful not to overmix the batter after adding eggs to avoid cracking during baking.
- Use a kitchen thermometer to accurately check meringue temperature for safety and texture.
- If you don’t have a torch, briefly broil the meringue under an oven broiler watching closely to avoid burning.
- Chilling the cheesecakes overnight will improve texture and flavor.

