Keto Cheesecake Cupcake – A Creamy, Low-Carb Treat

If you love cheesecake but want to keep things light and low-carb, these keto cheesecake cupcakes will make your day. They’re rich, creamy, and perfectly portioned, so you can enjoy dessert without second-guessing it. The crust has a gentle almond crunch, and the filling is smooth with just the right touch of sweetness.

They’re easy to prep, bake beautifully, and chill into a silky bite you’ll want to keep on hand. Make a batch for the week, for guests, or for those moments when you want something sweet and simple.

What Makes This Special

These cheesecake cupcakes deliver everything you love about classic cheesecake in a lighter, keto-friendly way. The almond flour crust keeps carbs low while adding a nutty base that pairs well with vanilla and lemon.

Each cupcake is perfectly portioned, which helps with mindful indulgence and easy serving. They also store well, so you can make them ahead and enjoy a stress-free dessert all week.

What You’ll Need

• For the crust:
  • 1 cup almond flour
  • 2 tablespoons granular erythritol or your favorite keto sweetener
  • 1/4 teaspoon ground cinnamon (optional)
  • Pinch of salt
  • 3 tablespoons unsalted butter, melted
  • 1/2 teaspoon vanilla extract
• For the filling:
  • 16 ounces cream cheese, softened (full-fat)
  • 1/2 cup powdered erythritol (or another powdered keto sweetener)
  • 2 large eggs, at room temperature
  • 1/3 cup sour cream
  • 1 teaspoon vanilla extract
  • 1 tablespoon lemon juice (fresh) and 1/2 teaspoon lemon zest (optional but brightens flavor)
  • Pinch of salt
• For topping (optional):
  • Fresh berries (raspberries, blueberries, or sliced strawberries)
  • Sugar-free chocolate shavings or a drizzle of sugar-free chocolate sauce
  • Whipped cream (unsweetened or lightly sweetened with keto sweetener)
• Equipment:
  • 12-cup muffin tin
  • Paper or silicone cupcake liners
  • Mixing bowls and a hand mixer (or stand mixer)
  • Measuring cups and spoons
  • Rubber spatula

How to Make It

1. Prep the pan. Line a 12-cup muffin tin with liners. Preheat your oven to 325°F (163°C).
2. Make the crust. In a bowl, mix almond flour, erythritol, cinnamon, and salt.
   

   Stir in melted butter and vanilla until it forms a sandy, moist mixture.

3. Press the crust. Divide the crust mixture among the liners (about 1 tablespoon each). Press firmly to form an even base. A flat-bottomed glass works well.
4. Par-bake. Bake the crusts for 6–8 minutes until lightly golden at the edges.
   

   Remove and cool while you make the filling.

5. Beat the cream cheese. In a mixing bowl, beat softened cream cheese on medium speed until smooth and fluffy, about 1–2 minutes. Avoid overbeating.
6. Add sweetener and salt. Mix in the powdered erythritol and a pinch of salt until fully incorporated and creamy.
7. Add eggs. Beat in the eggs one at a time on low speed. Mix just until combined to prevent excess air.
8. Finish the filling. Add sour cream, vanilla, lemon juice, and zest.
   

   Mix on low until smooth. Scrape down the sides to ensure an even blend.

9. Fill the cups. Spoon the filling over the crusts, almost to the top. Tap the pan gently to release any air bubbles.
10. Bake. Bake at 325°F (163°C) for 16–20 minutes.
    

    The centers should look set around the edges and slightly jiggly in the middle.

11. Cool gradually. Turn off the oven, crack the door, and let the cupcakes sit for 10 minutes. Then transfer to a rack to cool to room temperature.
12. Chill to set. Refrigerate for at least 2–3 hours, preferably overnight, until firm and creamy.
13. Top and serve. Add a few berries, a dab of whipped cream, or chocolate shavings if you like. Serve chilled.

Keeping It Fresh

These cupcakes store well in the fridge for up to 5 days.

Keep them in an airtight container to prevent odors from the fridge from affecting the flavor. For longer storage, freeze them on a baking sheet until solid, then transfer to a freezer-safe container for up to 2 months. Thaw overnight in the fridge for the best texture and flavor.

Benefits of This Recipe

• Low-carb and keto-friendly: Made with almond flour and keto sweetener to keep net carbs down.
• Built-in portion control: Cupcake size makes serving simple and helps avoid overdoing it.
• Make-ahead friendly: The flavor and texture get even better after chilling.
• Customizable: Easy to adapt with citrus, chocolate, or berry variations.
• Satisfying texture: Creamy filling with a lightly crunchy crust gives that classic cheesecake feel.

Common Mistakes to Avoid

• Using cold ingredients: Cold cream cheese can cause lumps.
  

  Make sure cream cheese and eggs are at room temperature.

• Overmixing the batter: Too much air leads to cracks and a spongy texture. Mix on low and stop when combined.
• Overbaking: If they’re fully set in the oven, they’re overdone. A slight jiggle in the center is ideal.
• Skipping the chill: Cheesecake needs time to set.
  

  Rushing this step can lead to a loose, less creamy texture.

• Unlined or ungreased tins: Always use liners or the cupcakes can stick and break apart.

Recipe Variations

• Lemon Blueberry: Add 1 teaspoon extra lemon zest to the filling and fold in 1/3 cup fresh blueberries before baking.
• Chocolate Swirl: Melt 1 ounce sugar-free dark chocolate and swirl a little into each cupcake before baking.
• Strawberry Cheesecake: Top with sliced strawberries and a spoon of reduced sugar-free strawberry sauce.
• Salted Caramel: Drizzle with a keto-friendly caramel sauce and finish with a light pinch of flaky salt.
• Pumpkin Spice: Mix 1/4 cup pumpkin puree and 1/2 teaspoon pumpkin spice into the filling; bake a minute or two longer if needed.
• Coconut Almond: Add 1/4 teaspoon almond extract to the filling and sprinkle toasted unsweetened coconut on top.

FAQ

Can I use a different sweetener?

Yes. A powdered erythritol blend works best for a smooth texture, but allulose or monk fruit blends are great too. If using allulose, the cupcakes may brown faster, so keep an eye on them.

Do I need a water bath?

No.

Because these are small, they bake evenly without a bain-marie. Gentle heat and proper cooling are enough to prevent cracks.

How can I tell when they’re done?

The edges should look set and the center should jiggle slightly when you nudge the pan. If the tops puff or crack, they’re likely overbaked.

Can I make these dairy-free?

You can try dairy-free cream cheese and use coconut cream instead of sour cream, but the texture may be softer.

Bake times may vary, so check a minute or two earlier.

What if I don’t have almond flour?

Finely ground almond meal can work, though the crust will be a bit coarser. Coconut flour is not a 1:1 swap and will be too absorbent for this crust.

Can I make mini cheesecake bites?

Yes. Use a mini muffin pan with liners.

Reduce the crust to about 1 teaspoon per cup and bake time to 10–12 minutes total, watching closely.

How do I prevent liners from sticking?

Use high-quality parchment liners or silicone liners. Let cupcakes chill completely before peeling the liner away.

What’s the best way to soften cream cheese quickly?

Cut the cream cheese into cubes and let it sit at room temperature for 30 minutes. In a pinch, microwave at 50% power in 10–15 second bursts, stirring between rounds until just soft.

Can I add protein powder?

You can add 1–2 tablespoons unflavored or vanilla whey isolate to the filling.

Don’t add too much or the texture can turn chalky.

What toppings are keto-friendly?

Fresh berries in moderation, sugar-free chocolate, chopped nuts, or lightly sweetened whipped cream all work well. Keep portions modest to stay within your carb goals.

In Conclusion

These keto cheesecake cupcakes are simple, dependable, and satisfy that creamy dessert craving without the carb overload. With an almond flour crust and a silky filling, they’re as good for a weekday treat as they are for a party platter. Keep a batch chilled, play with the variations, and enjoy a dessert that feels special and fits your goals.