Mini protein cheesecakes are the ultimate dessert for those who want to satisfy their sweet tooth while maintaining a healthy twist. If you have been searching for a way to enjoy the creamy, rich texture of a classic cheesecake without the typical calorie count, you have found the proven recipe you need.

Having tested this recipe over nine times, Sophie has perfected the ratio of 0% Greek yogurt to cream cheese, ensuring a triumph of texture that is both light and decadent. These aren’t just “diet” desserts; they are a remarkable treat that tastes like a fresh, gourmet bakery item. Whether you are hosting a family gathering or looking for a practical way to meal prep high-protein snacks for the week, these mini cheesecakes are a successful choice. By using a muffin tin for perfect portions, this recipe is helpful, simple, and absolutely stunning to serve.
Why You’ll Love This Mini Protein Cheesecakes Recipe
There is a reason this popular recipe is a favorite for home cooks who love American-style desserts but want a powerful nutritional profile.
- Portion Controlled: Using a muffin tin creates 12 perfectly sized servings, making it simple to stay on track with your goals.
- High-Protein Boost: The addition of 0% Greek yogurt adds a remarkable amount of protein while keeping the texture silky and fresh.
- Bright Flavor: The unique combination of vanilla and fresh lemon zest provides an uplifting and vibrant taste.
- Sturdy Crust: A simple buttery graham cracker base provides the ultimate crunch to contrast the creamy filling.
- Beginner Friendly: This is an informative and easy process—no complicated water baths are required for these mini versions!
Ingredients for Mini Protein Cheesecakes
To achieve a superior result, it is important to use quality ingredients at the right temperature.
The Graham Cracker Crust
- Graham Cracker Crumbs: 1 ½ cups (about 10 sheets). Use gluten-free crumbs for a healthy twist if needed.
- Salted Butter: 5 tablespoons (melted). This binds the crust and adds a lovely savory note.
The Cheesecake Filling
- Cream Cheese: 8 oz (room temperature). This is the authentic base of the dessert.
- 0% Greek Yogurt: ¾ cup (room temperature). Adds protein and a fresh tang.
- Granulated Sugar: ⅓ cup. Just enough for a wonderful sweetness.
- Eggs: 1 large egg plus 1 egg yolk for a richer and more beautiful set.
- Vanilla Extract: 1 teaspoon for a fresh aroma.
- Lemon Juice & Zest: 2 teaspoons of juice and up to ½ teaspoon of zest for a vibrant finish.
- Arrowroot Starch: 1 tablespoon. This is the expert secret to a stable, non-runny filling.
Ingredient Notes and Healthy Swaps
If you want to tailor this recipe further for your family, consider these helpful notes:
- Sugar Alternatives: You can substitute granulated sugar with an equal amount of erythritol or monk fruit sweetener for a stunning low-calorie version.
- Greek Yogurt: Ensure you use “plain” yogurt to keep the flavor authentic. Using a flavored yogurt might make the cheesecake too sweet or floral.
- Starch Choice: If you don’t have arrowroot starch, cornstarch works as an excellent and practical 1:1 replacement.
Step-by-Step Instructions
Follow these simple steps to ensure your mini cheesecakes are a successful hit.
Step 1 – Prepare and Bake the Crust
Preheat your oven to 350°F and line a 12-cup muffin tin. Mix your graham cracker crumbs with melted butter until they look like wet sand. Divide the mixture evenly among the liners and press down firmly. Bake for 5–6 minutes. This “par-baking” step is proven to keep the crust from getting soggy.
Step 2 – Beat the Cream Cheese
In a large bowl, beat the room-temperature cream cheese until it is completely smooth. This is important; if the cream cheese is cold or lumpy, your final cheesecake will have a “surprising” and unpleasant texture.
Step 3 – Combine the Filling
Add the Greek yogurt, egg, yolk, sugar, vanilla, lemon juice, and zest. Finally, add the arrowroot starch. Mix on low speed for only 30–60 seconds. Over-mixing at this stage can incorporate too much air, leading to cracks in your beautiful cheesecakes.
Step 4 – Fill and Bake
Divide the filling evenly over the cooled crusts. Bake for 17–20 minutes. You are looking for the edges to be set while the centers still have a very slight jiggle. They should not look wet, but they should not be browned either.
Step 5 – The Essential Chill
Cool the tin at room temperature for 30 minutes, then move it to the refrigerator. You must chill these for at least 3 hours. This is the ultimate secret to a successful set and a tasty result.
Pro Tips for Success
- Room Temperature is Key: Ensure your eggs, yogurt, and cream cheese are all at room temperature. This is the greatest way to prevent lumps.
- Don’t Over-mix: Once you add the eggs, keep the mixer on low. Too much air causes the cheesecakes to rise and then sink, creating a “surprising” dip in the middle.
- Use Paper Liners: This makes the cheesecakes easy to remove and serve without any sticking.
- Zest Before Juicing: It is much simpler to zest the lemon before you cut it in half to juice it!
- Press Firmly: Use the bottom of a small glass to press the crumbs into the liners for a sturdy and professional crust.
Flavor Variations
- Chocolate Swirl: Add a teaspoon of cocoa powder to a small portion of the batter and swirl it in for an amazing look.
- Berry Topped: Once set, top with a spoonful of the reduction from our Chocolate Raspberry Sandwich Cookies.
- Peanut Butter: For a unique twist, whisk in a tablespoon of peanut butter, inspired by our Peanut Butter Nutella Cookie Recipe.
- Red Velvet: Add a drop of red food coloring and a teaspoon of cocoa for a stunning holiday dessert.
Serving Suggestions
- Fresh Fruit: Serve with a fresh strawberry or a few blueberries on top of each mini cake.
- Whipped Cream: A small dollop of homemade whipped cream makes these look outstanding.
- Dessert Bar: These are beautiful when served alongside our White Chocolate Stuffed Cookies for a variety of textures.

Storage and Freezing Instructions
- Refrigerate: Keep in an airtight container for up to 4 days. They actually taste even better on day two!
- Freezing: These freeze wonderfully. Wrap them individually and freeze for up to 2 months. Thaw in the fridge overnight for the best texture.
Nutrition Facts (Per Serving)
| Nutrient | Amount |
| Calories | 160 |
| Protein | 6 g |
| Carbs | 14 g |
| Fat | 9 g |
| Fiber | 0.5 g |
| Sodium | 135 mg |
FAQ About Mini Protein Cheesecakes
Why did my cheesecakes crack?
Cracks are usually caused by over-beating the eggs or baking them for too long. To keep them beautiful, mix on low speed and pull them out as soon as the edges are set.
Can I use fat-free cream cheese?
We recommend using standard or 1/3-less-fat cream cheese for the best flavor. Fat-free cream cheese often has additives that can make the texture “surprising” and rubbery.
Is arrowroot starch necessary?
The starch helps bind the extra moisture from the Greek yogurt. It is a useful and expert addition that ensures your cheesecakes are successful and firm.
Can I make this as one large cheesecake?
This specific recipe is optimized for mini versions. If you want a large cake, you would need to adjust the bake time and use a water bath to ensure it is successful.
Can I use flavored yogurt?
It is best to use plain Greek yogurt. Flavored versions (like vanilla) often contain extra gums and sugars that can change the chemistry of the bake.
Final Thoughts
These Ultimate Mini Protein Cheesecakes are a wonderful example of how you can enjoy a beautiful dessert while keeping things fresh and healthy. This proven recipe is a triumph for any home cook looking to provide quality treats for their family. If you loved this high-protein dessert, be sure to try our Chocolate Protein Bars for your next successful snack!
PrintMini Protein Cheesecakes
Mini protein cheesecakes are light, creamy, high-protein desserts made with Greek yogurt and cream cheese on a buttery graham cracker crust. These individual cheesecakes bake quickly, chill perfectly, and deliver classic cheesecake flavor with a healthier twist.
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 3 hours 35 minutes
- Yield: 12 mini cheesecakes
- Category: Desserts
- Cuisine: American
Ingredients
**Graham Cracker Crust**
Graham cracker crumbs – 1½ cups
Salted butter, melted – 5 tablespoons
**Cheesecake Filling**
Cream cheese, room temperature – 8 oz
0% Greek yogurt, room temperature – ¾ cup
Granulated sugar – ⅓ cup
Egg – 1 large
Egg yolk – 1
Vanilla extract – 1 teaspoon
Lemon juice – 2 teaspoons
Lemon zest – up to ½ teaspoon
Arrowroot starch – 1 tablespoon
Instructions
**Prepare the Crust**
Preheat oven to 350°F. Line a 12-cup muffin tin. Mix graham cracker crumbs with melted butter until evenly moistened. Press firmly into liners and bake for 5–6 minutes. Let cool slightly.
**Beat Cream Cheese**
In a large bowl, beat room temperature cream cheese until completely smooth and lump-free.
**Mix Filling**
Add Greek yogurt, egg, egg yolk, sugar, vanilla, lemon juice, zest, and arrowroot starch. Mix on low speed for 30–60 seconds until just combined.
**Fill and Bake**
Divide filling evenly over crusts. Bake for 17–20 minutes until edges are set and centers have a slight jiggle.
**Chill**
Cool at room temperature for 30 minutes, then refrigerate for at least 3 hours before serving.
Notes
• All dairy and eggs must be room temperature for smooth batter.
• Do not overmix once eggs are added—this prevents cracking.
• Arrowroot starch can be replaced with cornstarch 1:1.
• Chill time is essential for proper texture and clean removal.
• Paper liners make serving easy and mess-free.




