If you’re looking for a truly swoon-worthy treat, Vanilla Bean Cheesecake Cupcakes are about to become your new obsession. These little wonders pack all the creamy, dreamy decadence of classic cheesecake into perfectly portioned cupcakes, complete with a buttery graham cracker crust and a fragrant burst of real vanilla bean. They’re easy enough to whip up for a weeknight sweet tooth, yet fancy enough to dazzle at any get-together. Trust me, once you’ve tasted these Vanilla Bean Cheesecake Cupcakes, you’ll understand why they’re my go-to for dessert emergencies and celebrations alike!

Ingredients You’ll Need
The beauty of these Vanilla Bean Cheesecake Cupcakes lies in their simple, high-quality ingredients. Each one brings something special to the party—tender crust, rich filling, or that unmistakable touch of vanilla elegance.
- Graham cracker crumbs: Use classic honey graham crackers for that nostalgic, golden crust, or swap in chocolate for a twist.
- Granulated sugar: Provides sweetness for both the crust and the luscious filling, ensuring every bite is just right.
- Unsalted butter (melted): Binds the crust together and adds rich, buttery flavor—make sure it’s fully melted for even mixing.
- Cream cheese (softened): The star of any cheesecake, full-fat cream cheese makes the cupcakes irresistibly creamy and smooth.
- Eggs (large): Add richness and structure, helping the cheesecake set to its classic velvety texture.
- Vanilla bean paste or 1 vanilla bean (scraped): Delivers those gorgeous black flecks and an intense, aromatic vanilla flavor you simply can’t get from extract alone.
- Sour cream: The secret weapon for tang and silkiness, making each cupcake light yet indulgent.
- All-purpose flour: Just enough to provide structure without sacrificing creaminess.
How to Make Vanilla Bean Cheesecake Cupcakes
Step 1: Prep Your Muffin Tin
Begin by preheating your oven to 325 degrees Fahrenheit. Line a standard 12-cup muffin tin with cupcake liners—this helps the cupcakes release easily and gives them those classic crinkled edges everyone loves.
Step 2: Make the Graham Cracker Crust
In a medium bowl, combine the graham cracker crumbs, 1/4 cup of granulated sugar, and melted unsalted butter. Mix everything well until the crumbs look like wet sand. Divide the mixture evenly among the liners—about a heaping tablespoon per cup—and press down firmly to create a solid base. A flat-bottomed glass works wonders for a tidy, compact crust.
Step 3: Beat the Cream Cheese Mixture
In a large bowl, use an electric mixer to beat the softened cream cheese and 2/3 cup of granulated sugar together until totally smooth and fluffy. Scrape the bowl well—no lumps allowed! Add eggs, one at a time, beating after each so the filling stays silky.
Step 4: Add the Vanilla and Finish the Batter
Stir in the vanilla bean paste (or scraped seeds from 1 vanilla bean), sour cream, and all-purpose flour. Fold gently until just combined. Don’t over-mix—the less you handle the batter, the smoother your Vanilla Bean Cheesecake Cupcakes will be!
Step 5: Fill and Bake
Divide the cream cheese mixture over the crusts, filling each liner about three-quarters full. Pop the tin into your preheated oven and bake for 18 to 22 minutes. You’re looking for centers that are just set but still have a slight jiggle. Remove from the oven and let the cupcakes cool in the pan for about 10 minutes, then transfer them to a wire rack to cool completely.
Step 6: Chill Until Set
Patience makes perfection—refrigerate your cooled cupcakes for at least 3 hours, or even overnight. This allows that delectably creamy custard to fully set and the flavors to develop. Once chilled, they’re ready to serve!
How to Serve Vanilla Bean Cheesecake Cupcakes

Garnishes
These little cheesecakes are stunning all on their own, but a finishing touch can make them truly memorable. Try a dollop of freshly whipped cream, a crown of fresh berries, or a delicate dusting of powdered sugar. For extra indulgence, drizzle with dark chocolate or a spoonful of berry compote just before serving.
Side Dishes
Since Vanilla Bean Cheesecake Cupcakes are indulgently rich and satisfying, keep sides light and simple to balance things out. A platter of seasonal fruit, a crisp sparkling beverage, or hot espresso all make lovely pairings for these creamy mini cheesecakes.
Creative Ways to Present
You can personalize your presentation to suit any mood or occasion. Serve cupcakes on a beautiful tiered stand at brunch, nestle them in colorful wrappers for a festive party, or pop a single cupcake in a fancy box for an adorable edible gift. If you’re feeling extra, add edible flowers or a sprinkle of sea salt for a gourmet twist.
Make Ahead and Storage
Storing Leftovers
Vanilla Bean Cheesecake Cupcakes keep beautifully in the refrigerator. Simply cover them loosely with plastic wrap or store in an airtight container, and they’ll stay fresh and creamy for up to four days—if they last that long!
Freezing
For longer storage, these cupcakes freeze surprisingly well. Once chilled and fully set, wrap each cupcake individually in plastic wrap, then pop them in a zip-top bag or freezer-safe container. They’ll keep their luscious texture for up to a month—just thaw in the fridge overnight before serving.
Reheating
Cheesecake is best enjoyed chilled, so there’s no need to reheat refrigerated cupcakes. If you’re thawing from the freezer, let them slowly come to fridge temperature for the best texture. Avoid microwaving, as it can make the filling weep and soften the crust.
FAQs
Can I use vanilla extract instead of vanilla bean paste?
Yes, you can substitute an equal amount of good quality pure vanilla extract, though you’ll miss out on the beautiful specks and intense vanilla flavor that real vanilla bean paste brings to Vanilla Bean Cheesecake Cupcakes.
Why do my cheesecake cupcakes crack?
Cracks usually happen when cheesecakes are overbaked or cool too quickly. For best results, bake just until the centers are set but still have a slight jiggle, and allow them to cool gradually at room temperature before refrigerating.
Can I swirl in other flavors before baking?
Absolutely! Swirl in raspberry preserves, lemon curd, or even a touch of chocolate hazelnut spread into each cupcake just before baking, for a unique twist on classic Vanilla Bean Cheesecake Cupcakes.
What’s the best way to soften cream cheese?
Let the cream cheese sit at room temperature for at least 30 minutes before mixing, or remove the foil and microwave in short 10-second bursts until soft (but not melted). This makes mixing a breeze and ensures a smooth batter.
Can I make these gluten free?
Yes! Replace the graham cracker crumbs with your favorite gluten-free variety, and use gluten-free all-purpose flour. The rest of the ingredients are naturally gluten free, making Vanilla Bean Cheesecake Cupcakes easy to adapt for dietary needs.
Final Thoughts
If you’re looking for a dessert that’s both homey and a little bit fancy, you can’t go wrong with Vanilla Bean Cheesecake Cupcakes. They’re creamy, flavorful, and guaranteed to impress, yet easy enough for bakers of any skill level. Give them a whirl—your friends and family will be begging you for the recipe!
Print
Vanilla Bean Cheesecake Cupcakes Recipe
- Total Time: 3 hours 42 minutes including chilling
- Yield: 12 cupcakes 1x
- Diet: Non-Vegetarian
Description
Indulge in the creamy decadence of these Vanilla Bean Cheesecake Cupcakes that offer a perfect balance of sweetness and tanginess in every bite. These mini cheesecakes are a delightful treat for any occasion.
Ingredients
Cupcake Crust:
- 1 1/2 cups graham cracker crumbs
- 1/4 cup granulated sugar
- 6 tablespoons unsalted butter, melted
Cheesecake Filling:
- 16 ounces cream cheese, softened
- 2/3 cup granulated sugar
- 2 large eggs
- 1 teaspoon vanilla bean paste or 1 vanilla bean, scraped
- 1/2 cup sour cream
- 2 tablespoons all-purpose flour
Instructions
- Prepare Cupcake Crust: Preheat oven to 325 degrees Fahrenheit and line a 12-cup muffin tin with cupcake liners. In a medium bowl, combine graham cracker crumbs, 1/4 cup sugar, and melted butter. Press the mixture evenly into the bottom of each cupcake liner to form the crust.
- Make Cheesecake Filling: In a large bowl, beat cream cheese and 2/3 cup sugar until smooth. Add eggs one at a time, mixing well after each addition. Stir in vanilla bean paste or scraped vanilla bean, sour cream, and flour until just combined.
- Assemble and Bake: Pour the cream cheese mixture over the crusts, filling each about 3/4 full. Bake for 18-22 minutes or until the centers are set but still slightly jiggly. Allow cupcakes to cool to room temperature, then refrigerate for at least 3 hours before serving.
Notes
- For extra flavor, swirl in fruit preserves or chocolate before baking.
- Use full-fat cream cheese for the creamiest texture.
- Store leftovers covered in the refrigerator for up to 4 days.
- Prep Time: 20 minutes
- Cook Time: 22 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 cupcake
- Calories: 320
- Sugar: 25 g
- Sodium: 180 mg
- Fat: 22 g
- Saturated Fat: 13 g
- Unsaturated Fat: 7 g
- Trans Fat: 0 g
- Carbohydrates: 20 g
- Fiber: 1 g
- Protein: 5 g
- Cholesterol: 90 mg