Blueberry Cheesecake Cupcakes
These blueberry cheesecake cupcakes are built on my go-to soft vanilla cupcake base – light, fluffy, and super easy to make. They’re filled with a homemade blueberry compote, topped with cream cheese buttercream, and finished with a toasted graham cracker crumble. Basically, blueberry cheesecake, but in cupcake form.
I love the mix of textures in these – soft cupcake, jammy blueberry filling, creamy frosting, and that little bit of crunch on top. They feel bakery-worthy, but everything comes together with simple ingredients and a few extra steps that are 100% worth it.
Ingredient notes & substitutions
See the recipe card at the end of this post for the full ingredient list & quantities.
These cupcakes use the same soft vanilla base as this soft vanilla cupcake base recipe – light, fluffy, and super versatile. Here are a few extra notes for the added ingredients:
- Blueberries are used for the homemade filling – both fresh and frozen will work. I usually use frozen.
- Cornstarch helps thicken the blueberry compote so it doesn’t soak into the cupcake.
- Graham crackers give the topping that toasty, cheesecake-like crunch. I use honey grahams, but cinnamon works too.
- Cream cheese is the base of the frosting. Make sure to use full-fat block cream cheese (not whipped or tub-style) for the best texture.
- Butter is used in the cupcake batter, frosting, and graham crumble. I recommend unsalted and room temperature for best results.
- Powdered sugar sweetens the frosting and helps it hold its shape. If it looks clumpy, give it a quick sift.
- Vanilla extract or vanilla bean paste adds warmth and flavor to both the cupcake and the frosting. I always recommend using pure vanilla if you can.
Step by step instructions
See the recipe card at the end of this post for the full recipe instructions.
This recipe starts with my Soft Vanilla Cupcake Base — if you haven’t made it yet, you can find the full recipe here. Once your cupcakes are baked and fully cooled, you’re ready to assemble!
STEP 1: Make the blueberry compote. In a small saucepan, cook blueberries, sugars, lemon juice, and cornstarch/water over medium heat until thickened and jammy. Set aside to cool completely.
STEP 2: Make the graham cracker crumble. Stir together crushed graham crackers, granulated sugar, a pinch of salt, and melted unsalted butter. Toast in the oven at 350 F for 10–12 minutes, until golden and fragrant. Let it cool before using.
STEP 3: Core the cupcakes. Use a small knife or cupcake corer to remove the center of each cupcake, going about 1/2 of the way down.
STEP 4: Fill with blueberry compote. Spoon the blueberry filling into each cupcake, just enough to reach the top of the cavity.
STEP 5: Add graham cracker crumble. Sprinkle the graham cracker crumble over the blueberry filling. It adds a toasty crunch and helps hold the frosting in place.
STEP 6: Make the cream cheese buttercream. Beat together cold cream cheese and room temperature butter until smooth and well combined. Slowly mix in the powdered sugar and vanilla extract, then whip until light and fluffy.
STEP 7: Frost and finish. Pipe the frosting onto each cupcake, then top with a little more graham cracker crumble and a spoonful of blueberry compote for a final touch.
Recipe FAQ
Yes! You can bake the cupcakes 1-2 days ahead and store them (unfilled and unfrosted) in an airtight container at room temperature. The compote, frosting, and graham crumble can all be made ahead and stored separately. Assemble the day you plan to serve.
A small paring knife works great to core the centers, but if you bake a lot, a cupcake corer makes the process super quick and even. Use a spoon or piping bag to add the compote.
Absolutely. This recipe works just as well with raspberries, strawberries, or even cherries – just keep the proportions the same when cooking down the filling.
Over-baking is the most common culprit, but measuring flour incorrectly can also lead to dry cupcakes. I always recommend using a kitchen scale – it’s the most accurate way to ensure soft, tender results. If you’re not using a scale, be sure to spoon and level your flour (never scoop!).
Baking in grams
I rely on gram measurements when testing recipes because they offer the highest level of accuracy (and less cleanup!). Unlike volume measurements, which can vary, grams provide a reliable and consistent standard. I carefully test all of my recipes using this kitchen scale, therefore I cannot guarantee the outcome when using volume measurements. However, volume measurements are available in the recipe card.
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Blueberry Cheesecake Cupcakes
Ingredients
Blueberry Compote
- 400 grams (3 cups) frozen wild blueberries
- 100 grams (½ cup) granulated sugar
- 100 grams (½ cup) light brown sugar
- 2 tablespoons lemon juice
- 1 tablespoon + 1 teaspoon cornstarch
- 1 tablespoon water
Graham Cracker Crumble
- 150 grams graham cracker crumbs, about 9 full sheets
- 50 grams (¼ cup) granulated sugar
- 1 pinch of salt
- 57 grams (¼ cup) unsalted butter, melted
Vanilla Cupcake Base
- 192 grams (1 1/2 cups) cake flour
- ½ teaspoon baking soda
- ½ teaspoon baking powder
- ½ teaspoon fine sea salt
- 1 tablespoon milk powder
- 57 grams (¼ cup) unsalted butter, room temperature
- 50 grams (¼ cup) vegetable oil
- 150 grams (¾ cup) granulated sugar
- 2 eggs, room temperature
- 1 tablespoon vanilla bean paste or vanilla extract
- 80 grams (1/3 cup) whole milk, room temperature
- 120 grams (½ cup) sour cream or yogurt, room temperature
Cream Cheese Buttercream
- 226 grams unsalted butter, room temperature
- 8 oz full-fat cream cheese, cold
- 360 grams powdered sugar
- 1 pinch of salt
- ½ tablespoon vanilla bean paste or extract
Instructions
Blueberry Compote
- In a pot over medium heat, combine the wild blueberries, granulated sugar, brown sugar, and lemon juice. Cover & let the blueberries defrost & the sugar melt while stirring occasionally.400 grams frozen wild blueberries, 100 grams granulated sugar, 100 grams light brown sugar, 2 tablespoons lemon juice
- Separately, stir together the cornstarch & water. Once the blueberry juices have released and the mixture is boiling, add the cornstarch mixture and stir to combine. Let simmer for 20-30 minutes until thickened.1 tablespoon + 1 teaspoon cornstarch, 1 tablespoon water
- This usually yields around 250 mL of jam. Let cool.
Graham Cracker Crumble
- Preheat oven to 350F and line a baking sheet with parchment paper. Set aside.
- Mix together the graham cracker crumbs, sugar, and salt. Stir in the melted butter until the mixture resembles wet sand.150 grams graham cracker crumbs, 50 grams granulated sugar, 1 pinch of salt, 57 grams unsalted butter
- Spread the mixture onto the baking sheet. Bake for 10-12 minutes until golden and aromatic.
Vanilla Cupcake Base
- Preheat oven to 350F and fill a cupcake tin with liners. Set aside.
- Whisk together the cake flour, baking soda, baking powder, salt, and milk powder. Set aside.192 grams cake flour, ½ teaspoon baking soda, ½ teaspoon baking powder, ½ teaspoon fine sea salt, 1 tablespoon milk powder
- Separately, beat together the unsalted butter, oil, and sugar until combined & fluffy.57 grams unsalted butter, 50 grams vegetable oil, 150 grams granulated sugar
- Add the eggs & vanilla and mix well, then add the dry ingredients and beat until almost combined.2 eggs, 1 tablespoon vanilla bean paste or vanilla extract
- Once almost mixed in, add the sour cream and mix until almost combined. Then, stream in the milk & beat until a smooth batter forms.80 grams whole milk, 120 grams sour cream or yogurt
- Fill each cupcake liner about half way. Bake for 13-15 minutes until risen and fluffy – a toothpick inserted into the center should come out clean or with a few moist crumbs.
Frost & Assemble
- While the cupcakes cool, make the cream cheese buttercream. Beat the butter & cream cheese on medium speed until combined & smooth. Add half of the powdered sugar and beat on low-medium speed until combined. Then add the salt, vanilla, and the other half of the powdered sugar and beat until combined.226 grams unsalted butter, 8 oz full-fat cream cheese, 360 grams powdered sugar, 1 pinch of salt, ½ tablespoon vanilla bean paste or extract
- Use a small knife or cupcake corer to remove the center of each cupcake, going about ½ of the way down.
- Spoon the blueberry filling into each cupcake, just enough to reach the top of the cavity.
- Sprinkle the graham cracker crumble over the blueberry filling. It adds a toasty crunch and helps hold the frosting in place.
- Pipe the frosting onto each cupcake, then top with a little more graham cracker crumble and a spoonful of blueberry compote for a final touch.
