Cheesecake cupcakes are a delightful twist on the classic dessert. They are creamy, indulgent, and perfectly portioned for any occasion. Whether you’re preparing for a celebration or simply treating yourself, these little bites of heaven are sure to impress. With the option of using either traditional or vegan cream cheese, you can cater to various dietary preferences without sacrificing flavor. The combination of smooth cream cheese, tangy yogurt, and a touch of sweetness creates a rich and satisfying treat. Plus, they’re easy to make and can be customized to suit your tastes!
Why This Recipe Works

This cheesecake cupcakes recipe is a winner for several reasons. First, the use of 12 oz cream cheese or vegan cream cheese ensures a luscious, creamy texture that’s essential for any cheesecake. The addition of plain yogurt, such as almond milk yogurt, adds a lovely tang and helps to lighten the overall flavor. The sweetener of choice allows for flexibility, making it easy to adjust the sweetness to your liking. Furthermore, cornstarch or almond flour provides stability to the cupcakes, ensuring they don’t crack during baking. Lastly, by using graham crackers as an optional crust, you create a delightful crunch that complements the creamy filling perfectly.
What You’ll Gather
- 12 oz cream cheese or vegan cream cheese – The star ingredient for a rich filling.
- 1 cup plain yogurt – Adds tanginess and creaminess.
- 1/3 cup sweetener of choice – Choose from sugar, xylitol, honey, or your favorite alternative.
- 1 tsp pure vanilla extract – Enhances the overall flavor.
- 2 tsp cornstarch (or 3 tbsp almond flour) – Provides structure to the cupcakes.
- Optional: 4-5 graham crackers – For a crunchy crust.
What You’ll Need (Gear)
- Muffin tin – To bake your cupcakes.
- Parchment liners – For easy removal and a neat presentation.
- Mixing bowl – To combine all the ingredients.
- Electric mixer – For a smooth and creamy batter.
- Measuring cups and spoons – For accurate ingredient measurements.
- Spatula – To scrape down the sides of the bowl.
Cook Cheesecake Cupcakes Like This

Step 1: Preheat the Oven
Begin by preheating your oven to 325°F (160°C). This ensures that your cheesecake cupcakes bake evenly.
Step 2: Prepare the Muffin Tin
Line a muffin tin with parchment liners. If you’re using graham crackers, crush them into fine crumbs and press about a tablespoon into the bottom of each liner to create a crust.
Step 3: Mix the Filling
In a mixing bowl, combine the 12 oz cream cheese or vegan cream cheese with the 1 cup plain yogurt, 1/3 cup sweetener, 1 tsp pure vanilla extract, and 2 tsp cornstarch. Using an electric mixer, beat until the mixture is smooth and creamy, scraping down the sides of the bowl as needed.
Step 4: Fill the Muffin Tin
Spoon the cheesecake mixture into the prepared muffin tin, filling each liner about 2/3 full.
Step 5: Bake
Place the muffin tin in the preheated oven and bake for 18-20 minutes, or until the edges are set, and the centers still have a slight jiggle.
Step 6: Cool
Remove the muffins from the oven and allow them to cool in the tin for about 10 minutes. Then, transfer them to a wire rack to cool completely.
Step 7: Chill
For the best flavor and texture, refrigerate the cheesecake cupcakes for at least 2 hours before serving. This allows them to firm up and develop a deliciously creamy consistency.
Spring to Winter: Ideas

- Add a fruit topping such as fresh strawberries or blueberries for a bright spring touch.
- In summer, drizzle with a homemade berry sauce for a refreshing dessert.
- For fall, mix in some pumpkin puree and spices for a cozy, seasonal twist.
- During winter, top with a rich chocolate ganache or serve with peppermint extract for a festive flair.
Troubles You Can Avoid
- Overmixing can lead to a dense texture; mix only until combined.
- Make sure to cool the cupcakes gradually to prevent cracks on the surface.
- Keep an eye on the baking time; overbaking can dry out the cupcakes.
- Letting the cupcakes chill is essential for achieving the right consistency.
Keep-It-Fresh Plan
These cheesecake cupcakes can be stored in the refrigerator for up to 5 days. To keep them fresh, make sure they are covered tightly with plastic wrap or stored in an airtight container. You can also freeze the cupcakes for up to 2 months. Simply thaw them in the refrigerator overnight before serving.
Handy Q&A
Can I make these cheesecake cupcakes gluten-free?
Absolutely! Simply use gluten-free graham crackers or omit the crust entirely for a crustless version. The filling will still be delicious!
Can I substitute the yogurt?
Yes, you can use any type of yogurt, including coconut yogurt or another non-dairy variety if you’re looking for a vegan option.
How can I add flavor variations to the cheesecake cupcakes?
Feel free to mix in various flavorings, such as lemon zest, cocoa powder, or even matcha powder for unique twists. Just be mindful of adjusting the sweetener if you’re adding additional ingredients.
What should I serve with these cheesecake cupcakes?
These cupcakes pair beautifully with a cup of coffee or tea. You can also serve them alongside a refreshing Chocolate Chip Cookie Cheesecake Bars for a delightful dessert spread.
Desserts to Finish
- Decadent Triple Chocolate Cheesecake – For chocolate lovers.
- Chocolate Chip Cookie Cheesecake Bars – A fun variation of cheesecake.
In Closing
Cheesecake cupcakes are the perfect dessert for any occasion. With their creamy texture and customizable flavors, they are sure to please any crowd. Whether you stick to the classic recipe or add your own twists, these little treats are a slice of heaven in cupcake form. Enjoy your baking adventure and the delicious rewards that come with it!

Cheesecake Cupcakes
Ingredients
- 12 oz cream cheese or vegan cream cheese the star ingredient for a rich filling
- 1 cup plain yogurt adds tanginess and creaminess
- 1/3 cup sweetener of choice choose from sugar, xylitol, honey, or your favorite alternative
- 1 tsp pure vanilla extract enhances the overall flavor
- 2 tsp cornstarch or 3 tbsp almond flour for structure
- 4-5 graham crackers optional for a crunchy crust
Instructions
- Step 1: Preheat the Oven. Begin by preheating your oven to 325°F (160°C). This ensures that your cheesecake cupcakes bake evenly.
- Step 2: Prepare the Muffin Tin. Line a muffin tin with parchment liners. If you're using graham crackers, crush them into fine crumbs and press about a tablespoon into the bottom of each liner to create a crust.
- Step 3: Mix the Filling. In a mixing bowl, combine the cream cheese or vegan cream cheese with the plain yogurt, sweetener, vanilla extract, and cornstarch. Using an electric mixer, beat until the mixture is smooth and creamy, scraping down the sides of the bowl as needed.
- Step 4: Fill the Muffin Tin. Spoon the cheesecake mixture into the prepared muffin tin, filling each liner about 2/3 full.
- Step 5: Bake. Place the muffin tin in the preheated oven and bake for 18-20 minutes, or until the edges are set, and the centers still have a slight jiggle.
- Step 6: Cool. Remove the muffins from the oven and allow them to cool in the tin for about 10 minutes. Then, transfer them to a wire rack to cool completely.
- Step 7: Chill. For the best flavor and texture, refrigerate the cheesecake cupcakes for at least 2 hours before serving. This allows them to firm up and develop a deliciously creamy consistency.
Equipment
- Muffin Tin
- Parchment liners
- Mixing Bowl
- Electric Mixer
- Measuring cups and spoons
- Spatula
Notes
- Store cheesecake cupcakes in the refrigerator for up to 5 days, covered tightly.
- Freeze for up to 2 months; thaw overnight in the refrigerator before serving.
- Consider adding a fruit topping for a seasonal twist.
