If you adore creamy, dreamy desserts that feel both indulgent and approachable, then this Vanilla Bean Cheesecake Cupcakes Recipe is your new best friend in the kitchen. These little beauties combine the rich, velvety texture of classic cheesecake with the convenience of a cupcake, making them perfect for sharing or savoring all on your own. Infused with real vanilla bean seeds and nestled in a perfectly buttery graham cracker crust, each bite bursts with a delightful balance of sweetness and depth that will have you reaching for just one more.

Ingredients You’ll Need
The magic of this Vanilla Bean Cheesecake Cupcakes Recipe lies in its simple, carefully chosen ingredients. Each one plays a crucial role—from the creamy softness of the cream cheese to the fragrant vanilla bean seeds that elevate every bite with delicate flavor.
- Graham cracker crumbs: Provide a crunchy, buttery base that adds texture and a hint of sweetness.
- Unsalted butter (melted): Binds the crust together while offering rich, smooth flavor.
- Granulated sugar: Sweetens both the crust and the cheesecake filling for perfect balance.
- Vanilla extract: Adds warmth and depth alongside the vanilla bean for intense vanilla flavor.
- Cream cheese (softened): The star of the show, delivering that classic cheesecake creaminess.
- Sour cream: Enhances the texture, keeping the cheesecake moist and silky.
- Large eggs: Help to set the cheesecake, giving it structure without making it dense.
- All-purpose flour: A little binder to ensure the filling sets just right.
- Vanilla bean (split and seeds scraped): The secret weapon for pure, fragrant vanilla flavor that shines through beautifully.
- Whipped cream: For topping, adding lightness and creamy sweetness.
- Fresh berries: Strawberries, blueberries, and raspberries provide a fresh, vibrant contrast.
- Chocolate shavings: Optional garnish that adds a touch of decadence and elegance.
How to Make Vanilla Bean Cheesecake Cupcakes Recipe
Step 1: Prepare the Oven and Pan
Start by preheating your oven to 325°F (160°C) and lining a standard muffin tin with cupcake liners. This sets the stage for your crust and ensures the cupcakes bake evenly without sticking.
Step 2: Mix the Crust
In a medium bowl, mix the graham cracker crumbs, melted butter, granulated sugar, and vanilla extract. Stir until all crumbs are moist and resemble wet sand. This mixture forms the sturdy base that adds a delightful crunch under the creamy filling.
Step 3: Form the Crust in Cupcake Liners
Press about one tablespoon of the crust mixture firmly into the bottom of each cupcake liner. This step is key for a sturdy yet tender crust that won’t crumble when you take a bite.
Step 4: Prebake the Crust
Bake the crusts for 8 to 10 minutes until lightly golden. Remove and allow them to cool. Prebaking prevents sogginess and locks in that golden flavor.
Step 5: Beat the Cream Cheese
In a large bowl, beat the softened cream cheese on medium speed until smooth and creamy, about 2 to 3 minutes. This ensures a luscious texture free of lumps.
Step 6: Add Sugar to the Cream Cheese
Beat in the granulated sugar until fully combined, scraping the bowl’s sides as needed. This step sweetens the filling evenly without graininess.
Step 7: Incorporate Sour Cream
Mix in the sour cream until smooth. It brings moisture and a slight tang that balances the sweet flavors.
Step 8: Add Eggs One by One
Carefully add eggs one at a time, mixing on low speed just until combined after each addition. This helps prevent overmixing while providing structure.
Step 9: Mix in Flour
Sprinkle the flour over the mixture and gently mix until just incorporated. The flour helps the filling hold its shape as it bakes.
Step 10: Add Vanilla Flavor
Stir in the vanilla extract and the precious seeds scraped from your split vanilla bean. This step fills the batter with irresistible vanilla aroma and taste.
Step 11: Fill the Cupcake Liners
Once the crusts have cooled, carefully spoon the cheesecake mixture into each liner, leaving about a quarter inch of space from the top to prevent overflow during baking.
Step 12: Remove Air Bubbles
Give the muffin tin a gentle tap on the counter to release any air pockets trapped in the batter for a smooth finish.
Step 13: Bake the Cupcakes
Bake for 18 to 20 minutes until the edges are firm but the centers still jiggle slightly when you gently shake the pan. This ensures a creamy center with perfect texture.
Step 14: Cool in Oven
Turn off the oven, crack the door open, and let the cupcakes cool inside for 30 minutes. This gradual cooling helps prevent cracks on the surface.
Step 15: Chill Completely
Remove the cupcakes from the oven, let them cool at room temperature, then refrigerate for at least 2 hours or overnight so the flavors meld beautifully and the texture firms up.
Step 16: Add Toppings
Before serving, top each cupcake with a generous dollop of whipped cream to add lightness and creaminess that complements every bite.
Step 17: Garnish with Fresh Berries
Finish with fresh berries atop the whipped cream for a pop of color, freshness, and a natural burst of sweetness that pairs perfectly with the richness of the cheesecake.
How to Serve Vanilla Bean Cheesecake Cupcakes Recipe

Garnishes
Besides the classic whipped cream and fresh berries, you can sprinkle chocolate shavings or a dusting of powdered sugar over the cupcakes to elevate their appearance and flavor. Edible flowers or a drizzle of raspberry sauce also make for stunning, mouthwatering garnishes.
Side Dishes
Pair these cupcakes with a cup of rich coffee, a smooth latte, or even a light herbal tea to balance the sweetness. A simple bowl of mixed fresh fruit works well too, keeping your dessert experience fresh and vibrant.
Creative Ways to Present
Transform these cupcakes into mini dessert parfaits by layering broken cupcake pieces with whipped cream and berries in a glass. Or arrange them on a tiered stand with varied toppings for an impressive dessert table display that’s sure to impress guests.
Make Ahead and Storage
Storing Leftovers
Vanilla Bean Cheesecake Cupcakes keep wonderfully in the refrigerator for up to 4 days when stored in an airtight container. This allows the flavors to develop even more, making each bite tastier than the last.
Freezing
You can freeze the cupcakes without toppings for up to 2 months. Wrap each cupcake individually in plastic wrap and place them in a freezer-safe container to maintain their texture and flavor. Thaw overnight in the refrigerator before serving.
Reheating
These cupcakes are best enjoyed chilled, so simply allow frozen cupcakes to thaw in the fridge. If you prefer them slightly warm, let them sit at room temperature for about 30 minutes, but avoid microwaving as it may affect texture.
FAQs
Can I use vanilla extract instead of a vanilla bean?
Absolutely! While the vanilla bean seeds add a beautiful speckled look and a more intense flavor, you can substitute an additional teaspoon of vanilla extract if beans are not available.
Do I need to use sour cream in the recipe?
Sour cream adds moisture and a subtle tang that balances the sweetness. You could replace it with Greek yogurt for a slightly different texture and tanginess, but sour cream is preferred for a classic result.
How do I prevent cracks on my cheesecake cupcakes?
Gradual cooling is key to avoiding cracks. That’s why we leave the cupcakes in the oven with the door cracked for 30 minutes after baking—it helps them cool evenly and gently.
Can I make these cupcakes gluten-free?
Definitely! Just swap the graham cracker crumbs for a gluten-free variety and use gluten-free all-purpose flour or cornstarch in the filling. The cupcakes will be just as delicious!
What’s the best way to make the crust stay crunchy?
Prebaking the crust and packing it firmly are essential. Also, letting the crust cool completely before adding the filling helps keep it from becoming soggy during baking.
Final Thoughts
If you’re searching for a dessert that’s both elegant and simple to make, this Vanilla Bean Cheesecake Cupcakes Recipe fits the bill perfectly. Whether for a special celebration or a cozy night in, these cupcakes offer all the classic cheesecake flavors in a delightful, portable form. Trust me, once you try them, they’ll become a constant favorite in your baking repertoire!
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Vanilla Bean Cheesecake Cupcakes Recipe
- Prep Time: 25 minutes
- Cook Time: 30 minutes
- Total Time: 2 hours 30 minutes
- Yield: 12 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
These Vanilla Bean Cheesecake Cupcakes are a delightful and creamy dessert perfect for satisfying your sweet tooth. Featuring a buttery graham cracker crust, a rich vanilla bean-infused cheesecake filling, and topped with whipped cream and fresh berries, they offer a perfect balance of flavors and textures in a convenient cupcake form.
Ingredients
Crust
- 1 ½ cups graham cracker crumbs
- ½ cup unsalted butter, melted
- ¼ cup granulated sugar
- 1 teaspoon vanilla extract
Cheesecake Filling
- 16 oz cream cheese, softened
- ½ cup granulated sugar
- ½ cup sour cream
- 2 large eggs
- 1 tablespoon all-purpose flour
- 1 teaspoon vanilla extract
- 1 vanilla bean, split and seeds scraped
Toppings
- Whipped cream
- Fresh berries (strawberries, blueberries, raspberries)
- Chocolate shavings
Instructions
- Preheat Oven and Prepare Tin: Preheat your oven to 325°F (160°C). Line a standard muffin tin with cupcake liners to ensure easy removal of the cupcakes.
- Make Crust Mixture: In a medium bowl, combine the graham cracker crumbs, melted butter, granulated sugar, and vanilla extract. Mix thoroughly until the crumbs are evenly coated and have the texture of wet sand.
- Press Crust in Liners: Using about 1 tablespoon of the crust mixture, firmly press it into the bottom of each cupcake liner to create an even crust base.
- Bake Crusts: Bake the crusts in the preheated oven for 8-10 minutes or until they turn lightly golden. Remove from the oven and let them cool completely.
- Beat Cream Cheese: In a large mixing bowl, beat the softened cream cheese with an electric mixer on medium speed for 2-3 minutes until smooth and creamy without lumps.
- Add Sugar and Mix: Add the granulated sugar to the cream cheese and beat again until the mixture is well combined, scraping down the sides as necessary to incorporate everything evenly.
- Incorporate Sour Cream: Mix the sour cream into the cream cheese mixture until fully blended, creating a smooth batter.
- Add Eggs Slowly: Add the eggs one at a time, mixing on low speed after each addition just until combined to prevent overmixing and maintain a creamy texture.
- Add Flour: Sprinkle in the all-purpose flour and mix gently until just combined to help stabilize the cheesecake.
- Incorporate Vanilla Bean: Add the vanilla extract along with the scraped seeds from the split vanilla bean. Mix the batter until the seeds and flavor are evenly distributed.
- Fill Cupcake Liners: Once the crusts have cooled, fill each cupcake liner with the cheesecake filling, leaving about ¼ inch of space at the top to allow for slight rising during baking.
- Remove Air Bubbles: Gently tap the muffin tin on the countertop to release any trapped air bubbles in the batter for a smooth finished texture.
- Bake Cheesecake Cupcakes: Bake the filled cupcake tin for 18-20 minutes, or until the edges are set but the centers still have a slight jiggle when shaken gently.
- Cool in Oven: Turn off the oven and crack the door open. Let the cupcakes cool gradually inside the oven for about 30 minutes to prevent cracking.
- Cool Completely: Remove the cupcakes from the oven and allow them to cool completely at room temperature before placing in the refrigerator.
- Chill: Refrigerate the cupcakes for at least 2 hours, preferably overnight, to let them set and develop their full flavor.
- Add Toppings: Once chilled, top each cupcake with a dollop of whipped cream, fresh berries such as strawberries, blueberries, and raspberries, and garnish with chocolate shavings for an elegant finish.
Notes
- Ensure cream cheese is fully softened to avoid lumps in the batter.
- Do not overbeat eggs into the batter to maintain a creamy texture.
- Cooling cupcakes gradually helps prevent cracks in the cheesecake.
- Use fresh berries for the best flavor and visual appeal.
- Store leftover cupcakes covered in the refrigerator for up to 3 days.