I remember when I first went gluten-free, dessert felt like a minefield. Could I still have my favorite treats without sacrificing flavor?
Cheesecake was my ultimate test. These cheesecake cupcakes came from my kitchen experiments and honestly—they’re perfect.
They’re creamy, tangy, and just sweet enough, all on top of a crumbly, buttery gluten-free crust. Whether you’re hosting friends or craving a midweek pick-me-up, these little gems hit the spot every time.
Tips for the Best Cheesecake Cupcakes
- Crust Tips: Use a food processor for consistent crumbs, or pop the crackers in a zip-top bag and crush them with a rolling pin.
- Room Temperature Ingredients: This prevents lumps in your filling and gives that perfect creamy texture.
- Flavor Variations: Swap lemon juice for lime or orange zest for a citrusy twist. Add 1 tbsp cocoa powder to the filling for a chocolate version.

Gluten-Free Cheesecake Cupcakes
- Total Time: 35 minutes
- Yield: 12 cupcakes 1x
- Diet: Gluten Free
Description
Creamy cheesecake cupcakes with a buttery gluten-free crust. Perfectly portioned, easy to make, and customizable with your favorite toppings.
Ingredients
For the Crust:
- 1 cup gluten-free graham cracker crumbs (about 10 crackers)
- 2 tbsp granulated sugar
- 4 tbsp unsalted butter, melted
For the Cheesecake Filling:
- 8 oz cream cheese, softened
- 1/3 cup granulated sugar
- 1 tsp pure vanilla extract
- 1 large egg
- 1 tbsp sour cream
- 1 tsp fresh lemon juice
- A pinch of salt
Optional Toppings:
- Fresh berries (strawberries, blueberries, raspberries)
- Whipped cream
- Drizzle of melted dark chocolate or caramel
Instructions
- Preheat and Prep: Set your oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners.
- Make the Crust:
- Combine the graham cracker crumbs, sugar, and melted butter in a bowl. Stir until the mixture resembles wet sand.
- Press about 1 tablespoon of the crust mixture into the bottom of each cupcake liner, packing it down firmly with the back of a spoon or a shot glass.
- Bake for 5 minutes and let cool while you prep the filling.
- Prepare the Cheesecake Filling:
- In a medium bowl, beat the cream cheese and sugar together with a hand mixer until smooth (no lumps, trust me—it’s worth the effort).
- Add the vanilla extract, egg, sour cream, lemon juice, and salt. Beat until just combined. Avoid overmixing; it keeps the texture silky.
- Assemble and Bake:
- Spoon the filling over the cooled crusts, dividing it evenly among the liners.
- Bake for 15–18 minutes, or until the centers are just set (a slight jiggle is fine).
- Cool the cupcakes in the pan for 10 minutes, then transfer to a wire rack. Chill in the fridge for at least 2 hours before serving.
- Serve and Garnish:
- Top with fresh berries, whipped cream, or a drizzle of chocolate for that extra wow factor.
Notes
Ensure ingredients are at room temperature for the best texture. Refrigerate leftovers in an airtight container for up to 5 days.
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 cupcake
- Calories: 180
- Sugar: 12g
- Sodium: 150mg
- Fat: 10g
- Saturated Fat: 6g
- Unsaturated Fat: 3g
- Trans Fat: 0g
- Carbohydrates: 20g
- Fiber: 1g
- Protein: 3g
- Cholesterol: 40mg