Imagine biting into a creamy, melt-in-your-mouth cheesecake with juicy blueberries and hints of vanilla—all in a convenient cupcake size! This gluten-free blueberry vanilla cheesecake recipe gives you that perfect indulgence, combining a crunchy crust with a smooth, rich filling topped with fresh blueberries. They’re ideal for gatherings or a treat-yourself dessert.
Ingredients
For the Crust:
- 1 cup gluten-free graham cracker crumbs – Provides a classic cheesecake base with a crumbly, buttery texture. Ensure the crumbs are gluten-free for a celiac-safe treat.
- 3 tbsp melted butter – Helps bind the crust and gives a rich, buttery flavor.
- 1 tbsp sugar – Adds a hint of sweetness to the crust.
For the Cheesecake Filling:
- 16 oz cream cheese, softened – The creamy base for the cheesecake; softened cream cheese blends smoother.
- ½ cup sugar – Sweetens the filling without overpowering the vanilla flavor.
- 2 large eggs – Provides structure and helps the cheesecake set properly.
- 1 tsp vanilla extract – Enhances the filling with a warm, aromatic flavor.
- 1 cup fresh blueberries – Adds a juicy pop of flavor and a beautiful purple hue throughout the cheesecake.
For the Topping:
- 1 cup blueberry compote or pie filling – Provides extra blueberry flavor on top, making the cupcakes look and taste indulgent.
How to Make Gluten-Free Blueberry Vanilla Cheesecake Cupcakes
Step 1: Prepare the Crust
- Preheat the oven to 325°F (160°C). Line a muffin tin with cupcake liners.
- In a bowl, mix the gluten-free graham cracker crumbs, melted butter, and sugar until well combined.
- Press about a tablespoon of the crust mixture into the bottom of each cupcake liner, pressing it down firmly with the back of a spoon.
- Bake the crusts for 5 minutes, then set aside to cool.
Step 2: Make the Cheesecake Filling
- In a large mixing bowl, beat the softened cream cheese and sugar until smooth and creamy.
- Add the eggs one at a time, beating well after each addition.
- Mix in the vanilla extract until evenly distributed.
- Gently fold in the fresh blueberries, distributing them evenly throughout the batter.
Step 3: Assemble and Bake
- Spoon the cheesecake filling over the cooled crusts in each cupcake liner, filling them almost to the top.
- Bake for 18-20 minutes or until the centers are just set but still have a slight jiggle.
- Turn off the oven, crack the oven door, and let the cheesecakes cool slowly for about 10 minutes. Then transfer to a wire rack to cool completely.
Step 4: Chill and Top with Blueberry Compote
- Refrigerate the cupcakes for at least 2 hours, or until fully chilled and set.
- Once ready to serve, top each cheesecake with a spoonful of blueberry compote or pie filling.
Frequently Asked Questions
Can I make these ahead of time?
Yes, these cheesecake cupcakes can be made up to 2 days in advance. Store them in an airtight container in the refrigerator, and top them with the compote just before serving.
Can I use frozen blueberries instead of fresh?
Yes, frozen blueberries can be used. Make sure to thaw and drain them well to prevent excess moisture in the batter.
What if I don’t have gluten-free graham crackers?
You can substitute with gluten-free digestive biscuits or crushed gluten-free cookies of your choice.
How do I know when the cheesecakes are done baking?
The centers should look set but still have a slight jiggle when you gently shake the pan. Overbaking can cause cracks.
Can I freeze these cheesecake cupcakes?
Yes, freeze the cupcakes without the compote topping for up to 2 months. Thaw overnight in the refrigerator, then top with compote before serving.
How can I make these dairy-free?
Use dairy-free cream cheese and a vegan butter substitute in the crust to make this recipe dairy-free.
What is the best way to soften cream cheese?
Leave it at room temperature for 30-45 minutes before starting. You can also microwave it for 10-15 seconds, but be careful not to overheat.

Gluten-Free Blueberry Vanilla Cheesecake Cupcakes Recipe
- Total Time: 40 minutes
- Yield: 12 cheesecake cupcakes 1x
Description
A creamy, delicious cheesecake cupcake with a juicy blueberry topping, perfect for a gluten-free indulgence!
Ingredients
- For the Crust:
- 1 cup gluten-free graham cracker crumbs
- 3 tbsp melted butter
- 1 tbsp sugar
- For the Cheesecake Filling:
- 16 oz cream cheese, softened
- ½ cup sugar
- 2 large eggs
- 1 tsp vanilla extract
- 1 cup fresh blueberries
- For the Topping:
- 1 cup blueberry compote or pie filling
Instructions
- Preheat oven to 325°F (160°C) and line a muffin tin with cupcake liners.
- Mix gluten-free graham cracker crumbs, melted butter, and sugar. Press a tablespoon into each liner. Bake for 5 minutes.
- Beat cream cheese and sugar until smooth. Add eggs one at a time, then vanilla. Fold in blueberries.
- Fill liners with cheesecake mixture, bake 18-20 minutes until set. Cool in the oven with the door cracked.
- Chill in the fridge for at least 2 hours. Top with blueberry compote before serving.
Notes
- Use softened cream cheese for a smooth texture.
- Substitute fresh blueberries with frozen if needed, but drain excess liquid.
- Refrigerate for 2 hours to set fully before serving.
- Prep Time: 15 minutes
- Cook Time: 25 minutes (including crust baking and cheesecake)