There is something truly magical about the combination of creamy, rich cheesecake and the convenience of a cupcake. This Vanilla Bean Cheesecake Cupcakes Recipe captures that magic perfectly. Each bite delivers a smooth, velvety cheesecake infused with the fragrant essence of fresh vanilla bean, all nestled on a buttery graham cracker crust. Whether you’re treating yourself or impressing friends, these cupcakes are the perfect sweet indulgence that feels both homemade and special.

Ingredients You’ll Need
The secret to outstanding cheesecake cupcakes lies in the simplicity and quality of your ingredients. Every item here plays a pivotal role in creating a dessert that’s creamy, flavorful, and irresistibly tender.
- Graham cracker crumbs: Provide the classic buttery crunch and a slightly sweet base for the crust.
- Unsalted butter: Melted for mixing with crumbs to bind the crust perfectly without overpowering saltiness.
- Granulated sugar: Adds essential sweetness to both crust and filling for the perfect balance.
- Vanilla extract: Enhances the overall flavor profile with warm, sweet notes.
- Cream cheese: The star ingredient, offering that rich, tangy smoothness only cheesecake can deliver.
- Sour cream: Adds a subtle tang and creamy texture to lighten the filling.
- Large eggs: Help bind everything together and lend structure to the cheesecake cupcakes.
- All-purpose flour: Stabilizes the filling for a flawless, luscious texture.
- Vanilla bean: The real vanilla seeds bring a depth and authenticity that elevates this recipe to gourmet status.
- Whipped cream: For topping, providing lightness and a touch of elegance.
- Fresh berries: Strawberries, blueberries, or raspberries add freshness and a burst of color.
- Chocolate shavings: Optional, but perfect for extra indulgence and texture contrast.
How to Make Vanilla Bean Cheesecake Cupcakes Recipe
Step 1: Prepare Your Oven and Cupcake Liners
Start by preheating your oven to 325°F (160°C) and lining a standard muffin tin with cupcake liners. This simple prep sets the stage for even baking and easy cleanup, making your experience much smoother.
Step 2: Mix the Crust Ingredients
In a medium bowl, combine graham cracker crumbs, melted butter, granulated sugar, and vanilla extract. Stir until the mixture looks like wet sand, ensuring all crumbs are evenly coated for a perfectly textured crust that holds together.
Step 3: Press the Crust into Liners
Firmly press about a tablespoon of crust mixture into the bottom of each cupcake liner. This step is crucial for creating a sturdy foundation that won’t crumble when you bite into your cheesecake cupcake.
Step 4: Bake and Cool the Crusts
Bake the crusts for 8 to 10 minutes until they turn a lovely light golden color. Then, allow them to cool completely on a wire rack. This step helps the crust set firmly before adding the cheesecake filling.
Step 5: Beat the Cream Cheese
Using an electric mixer, beat the softened cream cheese on medium speed until smooth and creamy, about 2 to 3 minutes. This is key for avoiding lumps and achieving that signature cheesecake silkiness.
Step 6: Add Granulated Sugar
Mix in the sugar thoroughly, scraping down the bowl as necessary to ensure even sweetness throughout your filling.
Step 7: Blend in the Sour Cream
Incorporate sour cream to create a lighter texture and subtle tanginess, which perfectly balances the richness of the cream cheese.
Step 8: Add the Eggs One at a Time
Carefully beat in the eggs, one by one, mixing slowly to prevent overbeating, which can cause cracking during baking.
Step 9: Incorporate the Flour
Sprinkle in the flour and mix just until combined. This will help stabilize the cheesecake filling and improve the cupcakes’ structure.
Step 10: Add Real Vanilla Bean and Extract
Stir in vanilla extract and the seeds scraped from the split vanilla bean. This is where the magic happens—those tiny black seeds infuse the filling with an unmistakable, aromatic vanilla flavor that makes this Vanilla Bean Cheesecake Cupcakes Recipe shine.
Step 11: Fill the Cupcake Liners
Spoon the creamy cheesecake mixture on top of the cooled crusts, leaving about ¼ inch of space at the top to allow the cupcakes to rise without overflowing.
Step 12: Remove Air Bubbles
Gently tap the muffin tin on your counter to release any trapped air bubbles. This helps the cupcakes bake evenly and remain smooth.
Step 13: Bake Until Just Set
Bake for 18 to 20 minutes until the edges look set but the centers still wobble slightly. This subtle jiggle means your cupcakes will have that perfect creamy texture without being dry.
Step 14: Cool Slowly in the Oven
Turn off the oven and leave the door slightly ajar, letting the cupcakes cool inside for 30 minutes. This slow cooling prevents cracks and helps the texture settle beautifully.
Step 15: Chill Completely
Remove the cupcakes and let them cool to room temperature before placing them in the refrigerator to chill for at least 2 hours, or ideally overnight. Chilling firms up the cheesecake, making it easier to handle and enhancing flavor depth.
Step 16: Add Whipped Cream
Once chilled, top each cupcake with a generous dollop of whipped cream. It adds a light, fluffy contrast that complements the dense cheesecake.
Step 17: Garnish with Fresh Berries
Add fresh strawberries, blueberries, or raspberries atop the whipped cream for a fresh burst of sweetness and eye-catching color that will impress anyone lucky enough to get a bite.
How to Serve Vanilla Bean Cheesecake Cupcakes Recipe

Garnishes
Beyond whipped cream and berries, you can elevate presentation with chocolate shavings, a drizzle of caramel sauce, or a sprinkle of toasted nuts. These garnishes not only taste amazing but add delightful textures that make each cupcake even more special.
Side Dishes
Serve your Vanilla Bean Cheesecake Cupcakes with a refreshing citrus salad or a cup of freshly brewed coffee or tea. The acidity and warmth of these accompaniments balance the richness of the cheesecake beautifully.
Creative Ways to Present
Consider serving these cupcakes on a tiered dessert stand for gatherings, or place individual cupcakes in rustic glass jars for a charming picnic vibe. You can also customize the toppings seasonally—think pumpkin spice in autumn or tropical fruit in summer.
Make Ahead and Storage
Storing Leftovers
Keep leftover cheesecake cupcakes in an airtight container in the refrigerator. They stay fresh and delicious for up to 4 days, making them ideal for enjoying over several days or sharing with friends.
Freezing
You can freeze these cupcakes to savor later. Wrap each one tightly in plastic wrap and place in a freezer-safe container. They will keep well for up to 2 months. When ready to eat, thaw overnight in the refrigerator.
Reheating
Cheesecake cupcakes are best enjoyed chilled, so reheating isn’t usually necessary. If you prefer a slightly warmer dessert, allow them to come to room temperature for about 30 minutes before serving.
FAQs
Can I use vanilla extract instead of fresh vanilla bean?
Absolutely! While fresh vanilla bean offers a more intense flavor and those beautiful specks, vanilla extract is a great substitute if you’re in a pinch. Use an extra teaspoon to boost the vanilla aroma.
Why do my cheesecake cupcakes crack on top?
Cracking usually happens if the oven temperature is too high or the cheesecake is overbaked. Baking low and slow, gently cooling in the oven, and not overmixing the batter are key to preventing cracks.
Can I make these gluten-free?
Yes! Use gluten-free graham cracker crumbs and ensure your flour substitute is a suitable 1:1 replacement for all-purpose flour to keep the texture intact.
How long should I chill the cupcakes before serving?
Chilling for at least 2 hours is essential for the best texture and flavor. Overnight chilling is even better, as it allows the flavors to meld and the cupcakes to firm up perfectly.
Can I double this recipe?
Definitely! This recipe is easily doubled for larger gatherings. Just be sure you have enough muffin tins and baking time may increase slightly with the larger batch.
Final Thoughts
Making this Vanilla Bean Cheesecake Cupcakes Recipe is a joyful experience that rewards you with luscious, elegant treats perfect for any occasion. I encourage you to give it a try—it’s a delightful way to impress guests or simply treat yourself to a dessert that feels wonderfully indulgent but is surprisingly easy to make. Once you taste that creamy vanilla bean filling paired with the crispy crust, I promise you’ll be hooked!
Print
Vanilla Bean Cheesecake Cupcakes Recipe
- Prep Time: 30 minutes
- Cook Time: 30 minutes
- Total Time: 3 hours (including chilling time)
- Yield: 12 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
These Vanilla Bean Cheesecake Cupcakes offer a creamy, luscious dessert with a buttery graham cracker crust and the fragrant sweetness of real vanilla bean. Perfectly portioned and topped with whipped cream and fresh berries, these cupcakes provide an elegant, indulgent treat to satisfy your sweet tooth.
Ingredients
Crust Ingredients
- 1 ½ cups graham cracker crumbs
- ½ cup unsalted butter, melted
- ¼ cup granulated sugar
- 1 teaspoon vanilla extract
Cheesecake Filling Ingredients
- 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 and prepare muffin tin: Preheat your oven to 325°F (160°C). Line a standard muffin tin with cupcake liners.
- Make the crust mixture: In a medium bowl, combine the graham cracker crumbs, melted butter, granulated sugar, and vanilla extract. Mix until the crumbs are evenly coated and resemble wet sand.
- Form crust in cupcake liners: Press about 1 tablespoon of the crust mixture into the bottom of each cupcake liner, packing it down firmly.
- Bake crusts: Bake the crusts for 8-10 minutes, or until lightly golden. Remove from the oven and let cool.
- Beat cream cheese: In a large mixing bowl, beat the softened cream cheese with an electric mixer on medium speed until smooth and creamy, about 2-3 minutes.
- Add sugar: Add the granulated sugar and beat until well combined, scraping down the sides of the bowl as needed.
- Incorporate sour cream: Mix in the sour cream until fully incorporated.
- Add eggs: Add the eggs one at a time, mixing on low speed after each addition until just combined.
- Add flour: Sprinkle in the flour and mix until just combined.
- Add vanilla: Add the vanilla extract and the seeds from the split vanilla bean, mixing until well incorporated.
- Fill cupcake liners: Once the crusts have cooled, fill each cupcake liner with the cheesecake mixture, leaving about ¼ inch of space at the top.
- Remove air bubbles: Gently tap the muffin tin on the counter to remove any air bubbles.
- Bake cheesecake cupcakes: Bake for 18-20 minutes, or until the edges are set but the centers still jiggle slightly.
- Cool in oven: Turn off the oven and crack the door open, letting the cupcakes cool in the oven for about 30 minutes.
- Chill: After 30 minutes, remove from the oven and let cool completely at room temperature. Transfer to the refrigerator to chill for at least 2 hours, or overnight.
- Add toppings: Once chilled, top each cupcake with a dollop of whipped cream.
- Garnish: Add fresh berries and chocolate shavings on top of the whipped cream for an extra touch of sweetness and elegance.
Notes
- Make sure the cream cheese is softened to room temperature to avoid lumps in the filling.
- Use full-fat cream cheese and sour cream for the creamiest texture.
- Do not overbake; the centers should still jiggle slightly to ensure a creamy consistency.
- Chilling the cupcakes overnight enhances flavor and texture.
- Vanilla bean seeds add a fragrant and authentic vanilla flavor, but you can substitute with 1 tablespoon vanilla extract if unavailable.
- Allowing the cupcakes to cool in the oven prevents cracking.

