
This mini protein keto cottage cheese cheesecake recipe transforms simple ingredients into decadent bite-sized treats without the guilt. Perfect for satisfying sweet cravings while staying on track with your keto or low-carb lifestyle, these cheesecakes deliver all the creamy richness you expect but with added protein benefits.
I created these mini cheesecakes during a particularly challenging diet phase when I was craving something sweet but needed to keep my macros in check. Now they've become my go-to dessert for both everyday treats and when entertaining health-conscious friends.
Ingredients
- Cottage cheese: Provides the perfect creamy base while adding significant protein content
- Greek yogurt: Enhances the tangy flavor profile while contributing additional protein
- Large eggs: Act as natural binders giving structure to these delicate treats
- Almond flour: Creates a nutty gluten-free crust alternative with minimal carbs
- Melted butter: Helps bind the crust and adds rich flavor
- Powdered erythritol: Delivers sweetness without spiking blood sugar
- Vanilla extract: Balances the tanginess with warm aromatic notes
- Salt: Enhances all flavors and balances the sweetness
- Fresh berries (optional): For a colorful antioxidant-rich topping
Step-by-Step Instructions
- Prepare Your Oven and Pan:
- Preheat your oven to exactly 325°F as this moderate temperature prevents the cheesecakes from cracking. Line each cup of your mini muffin tin with paper liners, making sure they're pressed firmly into the corners for even baking.
- Blend The Filling:
- Add cottage cheese, Greek yogurt, eggs, erythritol, vanilla extract, and salt to your blender or food processor. Run on high speed for 60-90 seconds, stopping once to scrape down the sides. The mixture should transform from lumpy to completely smooth with no visible cottage cheese curds.
- Create The Crust:
- Mix almond flour and melted butter in a medium bowl, using a fork to combine thoroughly. The mixture should resemble wet sand that holds together when pressed between your fingers. If it seems too dry, add an additional teaspoon of melted butter.
- Form The Base:
- Spoon approximately one teaspoon of the almond flour mixture into each muffin cup. Use the back of a measuring teaspoon or your fingers to press down firmly, creating a compact even layer across the bottom of each cup.
- Fill The Cups:
- Pour or spoon the cottage cheese mixture over each crust, filling each cup about 90% full. The cheesecakes will rise slightly during baking but settle as they cool.
- Bake To Perfection:
- Place the muffin tin in the center rack of your preheated oven and bake for 15-20 minutes. The tops should appear set but will still have a slight jiggle in the center. Avoid overbaking as this can cause the texture to become dry.
- Cool And Set:
- Remove from the oven and allow the cheesecakes to cool in the pan for 15 minutes before transferring to the refrigerator. Chill for at least 2 hours or preferably overnight to develop the best texture and flavor.

The cottage cheese is truly the star ingredient here. When I first tried using it in cheesecake, I was skeptical, but the blending process transforms those humble curds into something remarkably similar to traditional cream cheese filling, but with added nutritional benefits that make these little treats practically virtuous.
Making Ahead and Storage
These mini cheesecakes actually improve with time as the flavors meld together in the refrigerator. For best results, make them a day before serving. Store in an airtight container in the refrigerator for up to 5 days. If freezing, wrap each cooled cheesecake individually in plastic wrap, then place in a freezer bag. Thaw overnight in the refrigerator before serving.

Flavor Variations
The beauty of this basic recipe is how easily it can be customized. Add 1 tablespoon of lemon zest and 2 tablespoons of lemon juice for a citrus version. For chocolate lovers, incorporate 2 tablespoons of unsweetened cocoa powder into the filling. Spice enthusiasts might enjoy adding ½ teaspoon of cinnamon and a pinch of nutmeg for a warming twist. Each variation adds minimal carbs while completely transforming the flavor profile.
Nutritional Benefits
These mini cheesecakes offer substantial nutritional advantages over traditional desserts. The combination of cottage cheese and Greek yogurt creates a protein-rich base that helps stabilize blood sugar and provides lasting satiety. The almond flour crust delivers healthy fats and fiber, while keeping carbohydrates minimal. Each serving contains approximately 120 calories, 8g protein, 9g fat, and only 3g net carbs, making them suitable for various dietary approaches beyond just keto.
Serving Suggestions
While these cheesecakes are delicious on their own, they can be elevated with thoughtful toppings. A light dusting of additional powdered erythritol adds sweetness and visual appeal. Fresh berries provide a juicy contrast to the creamy filling. For special occasions, a dollop of whipped heavy cream or coconut cream turns these into elegant desserts. Serve them slightly chilled rather than cold from the refrigerator to allow the full flavor to come through.
Frequently Asked Questions
- → Can I use a different base flour?
Yes, you can substitute almond flour with coconut flour but use only half the amount, as coconut flour absorbs more liquid.
- → Can I use a different sweetener?
Absolutely! Replace powdered erythritol with monk fruit, stevia, or your preferred keto-friendly sweetener. Adjust to taste.
- → How do I know when the cheesecakes are done?
The mini cheesecakes are ready when the tops are set and slightly golden. They should not jiggle excessively in the center.
- → How should I store these cheesecakes?
Store the cheesecakes in an airtight container in the refrigerator for up to 5 days. Avoid leaving them out for extended periods.
- → Can I freeze these cheesecakes?
Yes, you can freeze them. Store in a freezer-safe container for up to 2 months. Thaw in the fridge before serving.