Bright, tangy, and secretly indulgent — these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe are a sunny twist on classic cupcakes.
They bake up light and tender with a creamy cheesecake center that surprises every bite.
Perfect for spring gatherings, weeknight treats, or when you need a showstopping dessert fast.
If you love cheesecake meets cupcake, you’ll want to stash this recipe alongside your favorite cheesecake recipes like the San Sebastian cheesecake for batch-baking days.
Why You’ll Love This Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Bright lemon flavor from both juice and zest for balanced citrus notes.
- Moist, tender crumb thanks to sour cream and a careful creaming method.
- Creamy cheesecake center adds a surprise texture contrast.
- Light, fluffy lemon buttercream that pipes beautifully.
- Easy to scale and perfect for parties or gifting.
- Make-ahead friendly: components can be prepped in advance.
These cupcakes combine a snappy lemon cake with a rich, velvety cheesecake core and a pillowy lemon frosting. The cake is tender, the filling is silky, and the frosting ties it together with bright acidity and sweetness. Expect a balanced bite where sugar and citrus are in harmony, and texture plays a starring role.
"These were the highlight of our brunch — light cake, creamy center, and the lemon frosting was perfect. Five stars!" — A delighted reader
Key Ingredients for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Unsalted butter (softened)
Unsalted butter controls the fat and flavor baseline in both the cupcakes and the frosting. Buy European-style butter for a slightly richer taste; avoid salted butter unless you adjust added salt. If you substitute with margarine, expect weaker structure and less flavor depth.
Fresh lemon juice and lemon zest
Fresh lemon juice and zest deliver volatile oils and bright acidity that bottled juice can’t match. Use unwaxed lemons and zest before juicing for maximum aromatic intensity. Substituting bottled lemon juice results in a flatter, less vibrant lemon profile.
Cream cheese (softened)
Cream cheese creates the silky cheesecake filling and adds tang to the frosting if used. Choose full-fat cream cheese for stability and flavor; low-fat versions can be runny and less flavorful. If you swap for mascarpone, expect a milder tang but a silkier mouthfeel.
All-purpose flour
All-purpose flour gives structure while letting the cupcakes remain tender when combined with sour cream. For a lighter crumb, sift the flour and measure by spooning into the cup. Using cake flour will yield even more tender cupcakes, while bread flour makes them dense.
Full Ingredient List for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- 1 1/2 cups all-purpose flour
- 1 teaspoon baking powder
- 1/4 teaspoon baking soda
- 1/4 teaspoon salt
- 1/2 cup unsalted butter (softened)
- 3/4 cup granulated sugar
- 2 large eggs
- 1 teaspoon vanilla extract
- 2 tablespoons fresh lemon juice
- 1 tablespoon lemon zest
- 1/2 cup sour cream
- 1/4 cup milk
- 4 oz cream cheese (softened)
- 2 tablespoons granulated sugar (for filling)
- 1/2 teaspoon vanilla extract (for filling)
- 1/2 cup unsalted butter (softened, for frosting)
- 2 cups powdered sugar
- 2 tablespoons lemon juice (for frosting)
- 1 tablespoon lemon zest (for frosting)
- 1–2 tablespoons milk (as needed for consistency)
Step-by-Step Instructions for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Step 1: Make the cheesecake filling
In a small bowl, combine the softened cream cheese, 2 tablespoons granulated sugar, and 1/2 teaspoon vanilla extract. Mix until the mixture is smooth and creamy, stopping when lumps are gone. Set this filling aside while preparing the cupcakes.
Pro Tip: The filling should be glossy, smooth, and hold its shape when scooped with a teaspoon.
Step 2: Prep oven and pan
Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper cupcake liners for easy removal and cleanup.
Pro Tip: The oven should be fully preheated; a stable 350°F yields even rise and sets the cheesecake center.
Step 3: Whisk dry ingredients
In a medium bowl, whisk together the all-purpose flour, 1 teaspoon baking powder, 1/4 teaspoon baking soda, and 1/4 teaspoon salt to ensure even distribution of leavening agents and salt.
Pro Tip: The dry mix should look uniform with no clumps; whisking aerates it for better lift.
Step 4: Cream butter and sugar
In a large bowl, beat the softened 1/2 cup unsalted butter and 3/4 cup granulated sugar together until the mixture is light and fluffy, about 3–4 minutes. This aerates the batter and creates a tender crumb.
Pro Tip: Proper creaming results in a pale, billowy mixture that leaves visible ribbon trails when the beater is lifted.
Step 5: Add eggs and flavor
Add the eggs one at a time, mixing well after each addition to fully incorporate. Then blend in 1 teaspoon vanilla extract, 2 tablespoons fresh lemon juice, and 1 tablespoon lemon zest to infuse citrus flavor throughout the batter.
Pro Tip: The batter should look homogenous and slightly glossy with lemon specks evenly distributed.
Step 6: Add sour cream and milk
Stir in the 1/2 cup sour cream and 1/4 cup milk, which add moisture and richness, making the cupcakes tender and soft.
Pro Tip: The batter should be smooth and pourable but not thin; it should hold a soft peak when scooped.
Step 7: Combine dry and wet
Gradually add the dry ingredients to the wet ingredients, mixing just until combined. Be careful not to overmix to keep the cupcakes light.
Pro Tip: Stop mixing once streaks of flour disappear; the final batter should be slightly thick and glossy.
Step 8: Fill liners and add cheesecake
Spoon about 1 tablespoon of cupcake batter into each liner. Place 1 teaspoon of the cheesecake filling in the center of each, then cover with more batter until the liners are about three-quarters full, sealing in the cheesecake surprise.
Pro Tip: Each liner should have a neat cheesecake dollop fully enclosed and the top batter should be smooth and even.
Step 9: Bake
Bake in the preheated oven for 18–22 minutes, or until the tops feel set and a toothpick inserted near the edge (not center) comes out clean. This ensures the cupcakes are properly baked without disturbing the cheesecake filling.
Pro Tip: The tops should spring back slightly and be pale golden; avoid overbrowning.
Step 10: Cool completely
Remove cupcakes from the oven and let them cool completely in the pan on a wire rack to prevent the filling from leaking and to prepare for frosting.
Pro Tip: Cooling in the pan for 10 minutes then transferring to a rack prevents the centers from collapsing.
Step 11: Make the lemon frosting
In a large bowl, beat the softened 1/2 cup butter until smooth. Gradually add 2 cups powdered sugar one cup at a time, mixing well after each addition. Stir in 2 tablespoons lemon juice and 1 tablespoon lemon zest for citrus brightness. Add 1 to 2 tablespoons of milk as needed to achieve a piping consistency. Beat the frosting until it is light and fluffy.
Pro Tip: The frosting should be glossy and hold soft peaks; add milk a little at a time for perfect consistency.
Step 12: Frost and garnish
Using a piping bag or spatula, frost the cooled cupcakes generously. For an elegant touch, garnish with additional lemon zest or a small lemon wedge if desired.
Pro Tip: The frosting should pipe smoothly and keep stiff ridges without drooping.
Expert Tips for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Temperature tips: Use room-temperature eggs, butter, and cream cheese for smooth incorporation and even texture.
- Batter texture: The cupcake batter should be thick but scoopable; if too thin, the cheesecake center can sink and leak.
- Cheesecake filling consistency: Keep the filling chilled if your kitchen is warm; warm filling will ooze during baking.
- Oven accuracy: Use an oven thermometer to ensure 350°F accuracy — many ovens run hot or cold.
- Equipment tips: A standard 12-cup muffin tin and an electric mixer make the process easier and more consistent.
- Piping tips: Chill the frosting briefly if it’s too soft before piping for cleaner swirls.
- Common mistakes: Overmixing the batter creates tunnels and dense cupcakes; mix only until combined.
- Visual checks: If cupcake tops crack excessively, your oven may be too hot or the batter overmixed.
For a pro-level frosting technique, try the same lavender-cream approach used in recipes like the lavender cream cheese frosting technique.
Storage & Freezing for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Store unfrosted cupcakes in an airtight container at room temperature for up to 24 hours. For longer fridge storage, place frosted cupcakes in a shallow airtight container and refrigerate for up to 4 days.
For freezer storage, freeze unfrosted cupcakes in a single layer on a baking sheet until solid, then transfer to a freezer-safe container or bag for up to 3 months. Thaw overnight in the refrigerator before bringing to room temperature.
If you need to freeze frosted cupcakes, flash-freeze them on a sheet pan, then wrap individually in plastic wrap and store in a rigid container for up to 2 months.
To reheat, bring to room temperature for 30–60 minutes; warm very briefly in a 300°F oven for 5–7 minutes if you prefer them slightly warm, but avoid heating frosted cupcakes directly.
For tips on storing cheesecakes and similar desserts, see how others manage longer-term storage like in the peppermint bark cheesecake storage guide.
Variations & Substitutions for Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Lemon-Blueberry: Fold 1/2 cup fresh blueberries into the cupcake batter for bursts of fruity sweetness; bake as directed and expect slightly more moisture in the crumb. This gives a juicy contrast to the cheesecake core and works well with a sprinkle of coarse sugar on top.
- Lavender Lemon: Add 1/2 teaspoon culinary lavender infused into the milk before adding to the batter for a floral note; strain before use for a smooth batter. The frosting can be tweaked with a small pinch of lavender sugar for a delicate finish.
- Lemon Curd Swirl: Spoon a small dollop of lemon curd on top of the cheesecake filling before sealing with batter to intensify citrus tang. The curd caramelizes slightly at the edges and creates a sticky, glossy pocket.
- Gluten-free: Swap the all-purpose flour for a 1:1 gluten-free blend with xanthan gum and reduce mixing to prevent a gummy texture. Expect slight changes in crumb and be sure to measure by weight for best results.
Frequently Asked Questions About Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Can I make the cheesecake filling ahead of time?
Yes. Mix the cream cheese filling and store it in an airtight container in the refrigerator for up to 48 hours. Bring it to room temperature and re-whip lightly before portioning so it regains a smooth, pipeable texture.
Why did my cheesecake filling leak out of the cupcake?
Leaking usually happens when the filling is too warm, the batter layer is too thin, or the oven temperature is too high. Chill the filling, use a thicker batter base under and over the filling, and confirm your oven is at 350°F to reduce leaks.
Can I use boxed cake mix instead of making the batter from scratch?
You can, but boxed mixes vary in moisture and structure; add sour cream (about 1/2 cup) to improve tenderness and follow batter thickness cues. Expect differences in crumb and flavor complexity compared to scratch.
How can I make the frosting less sweet but still pipeable?
Reduce powdered sugar slightly and increase lemon juice or a touch of cream cheese for tang; chill briefly if it becomes too soft. Add powdered sugar back in small amounts until the desired stiffness for piping is reached.
Are these cupcakes freezer-friendly after frosting?
Yes, if flash-frozen first. Place frosted cupcakes on a tray, freeze until solid, then wrap individually and store in a rigid container for up to 2 months. Thaw in the refrigerator before serving to preserve frosting texture.
Final Thoughts on Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
If you loved this recipe, please leave a star rating in the recipe card below and pin it to Pinterest for later. For a classic version with photos and step-by-step notes, I also like the original Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting post. For a fruity spin with blueberries, check this inspiring Cheesecake Stuffed Lemon Blueberry Cupcakes – Tornadough Alli version. If you want more lemon cupcake ideas and curd-based fillings, browse Lemon Cupcakes with Lemon Curd | Fresh Bean Bakery.
Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting
Ingredients
Method
- Step 1: Make the cheesecake filling by combining softened cream cheese, sugar, and vanilla extract until smooth. Set aside.
- Step 2: Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners.
- Step 3: Whisk together the flour, baking powder, baking soda, and salt in a bowl.
- Step 4: In a large bowl, cream together the softened butter and granulated sugar until light and fluffy.
- Step 5: Add eggs one at a time, blending well after each addition. Incorporate vanilla, lemon juice, and zest.
- Step 6: Stir in sour cream and milk until smooth.
- Step 7: Gradually mix the dry ingredients into the wet ingredients until just combined.
- Step 8: Fill cupcake liners with batter and add a teaspoon of cheesecake filling in the center, then cover with more batter.
- Step 9: Bake for 18–22 minutes until set; a toothpick should come out clean from the edge.
- Step 10: Cool completely in the pan before transferring to a wire rack.
- Step 11: For frosting, beat butter until smooth. Gradually add powdered sugar, stirring in lemon juice and zest until fluffy.
- Step 12: Frost cooled cupcakes with lemon frosting.