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Home » Recipes » Desserts

High Protein Cheesecake

Published: Jul 1, 2024 · Modified: May 13, 2025 by Megan

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This High Protein Cheesecake is a low-fat treat to enjoy any time the craving strikes. They're made with Greek yogurt, less sugar, and taste so creamy and delicious! This healthy cheesecake recipe will soon become your favorite dessert recipe! It's also Gluten Free + Low Calorie

A Mini Protein Cheesecake on a plate with a bite missing.
Jump to:
  • Why You Will Love This Low Calorie Cheesecake
  • Ingredients
  • How To Make Healthy Protein Cheesecake
  • Expert Tips
  • Storing Tips
  • Recipe FAQs
  • More Low Calorie Dessert Recipes
  • High Protein Cheesecake

I have a lot of protein recipes like protein donuts, protein overnight oats, and protein cookie dough to name a few, but this protein cheesecake recipe is my all-time favorite!

This low calorie cheesecake recipe is made with fat-free Greek Yogurt, light cream cheese, egg, lemon, and a buttery graham cracker crust. They're light, smooth, and creamy. Even better, they're made better for you and are pre-portioned for a healthier dessert option!

Why You Will Love This Low Calorie Cheesecake

  • Healthy Cheesecake Option: A typical slice of cheesecake has 40+ grams of fat and can run anywhere from 400-1000 calories per serving! This low-calorie cheesecake clocks in at 5 grams of fat total and 122 calories per serving!
  • Higher Protein and Lower Sugar: This healthy cheesecake recipe has 4 grams of protein and just 7 grams of sugar! These are much better than most dessert recipes.
  • Easy to Make: Making these protein cheesecake bites is easier than you think! This recipe is perfect for any level baker.
  • Versatile Dessert: Enjoy it as a weeknight dessert treat or serve it up to guests for a weekend dinner get-together.

Ingredients

Here's what you need to make this delicious high-protein cheesecake recipe! Scroll to the recipe card at the bottom of the blog post for the ingredient measurements, full instructions, nutritional data and to print this recipe.

Ingredients to make healthy cheesecake with greek yogurt on the table before mixing up.
  • Cream Cheese: I used light cream cheese for these healthy cheesecake bites. I do not recommend using full-fat cream cheese or whipped cream cheese. Neufchatel cream cheese is another option that has a third less fat than regular cream cheese which you can use.
  • Greek Yogurt: Use nonfat Greek yogurt to keep this a low-fat cheesecake. I do not recommend using full fat or low fat for this recipe or a dairy-free substitute for the recipe. There are no substitutes for this as it would require a completely different recipe.
  • Coconut Sugar: Adds sweetness to the cheesecake. You can use light brown sugar which is similar in terms of color and flavor. Other options include Swerve or another sugar substitute. You can also omit the sugar if you like.
  • Egg and Egg Yolk: This combination will create the consistency of the cheesecake when it's baked.
  • Vanilla Extract: Use pure vanilla extract for the best flavor.
  • Arrowroot Powder: This ingredient is used to thicken the cheesecake to the perfect consistency. You can use cornstarch or tapioca flour instead but you cannot omit it.
  • Lemon Juice and Zest: These add a bit of acid to balance the sweetness as well as add flavoring to the cheesecake. Add more zest to increase the lemon flavor without making it overly acidic.
  • Graham Crackers: These shape the crust of our Greek yogurt cheesecake. For gluten free you can use almond flour, which also boosts the protein, or use gluten-free graham crackers.
  • Butter: Mixed with the cookies to form the crust. It's important to moisten them and help them stay together.

NOTE: Please remember when you make substitutions, it does change the nutritional values from what you see in the recipe card below.

How To Make Healthy Protein Cheesecake

It's simple to make these mini cheesecakes! Here's how...

graham cracker crumbs in a food processor

Step One: Make the crust by pulsing the graham crackers in a food processor. Add the butter and pulse to combine.

Protein cheesecake filling is mixed in a bowl.

Step Two: Press the crust into your lined muffin cavities and bake until golden brown.

baked mini cheesecakes in muffin tin

Step Three: Make the filling as the crust bakes.

Healthy cheesecake batter poured on top of the crust in a muffin pan.

Step Four: Top the filling on top of the baked crust then bake again until the filling has set.

PRO TIP: You will also need a muffin tin with muffin liners. Silicone liners work best because the cheesecakes pop right out of them. Paper liners do not work as well as they get stuck.

Step Five: Remove from the oven and chili at room temperature for 30 minutes then refrigerator to set the cheesecakes for a minimum of 4 hours.

Mini protein cheesecake bites on a white platter topped with berries and whipped cream.

Expert Tips

  • Use Room Temperature Ingredients: When the eggs, lemon juice, cream cheese, and yogurt are at room temperature this ensures your cheesecake is perfectly smooth and has the right texture. Using cold ingredients will increase the baking time and potentially they will turn out under-baked.
  • Do Not Over Mix The Filling: Beat the filling just until the ingredients are combined otherwise the filling will be tough.
  • Do Not Over Bake: Remove the mini protein cheesecakes from the oven once the filling has set and is not jiggling. Over-baked cheesecakes will not be as creamy and will be more sponge-like.
  • Make Ahead: These cheesecakes are best made 24 hours in advance of serving. They require at least 4 hours of chilling but if they can set in the refrigerator overnight it's even better!
  • Serving: Serve your low-calorie cheesecake chilled with fresh berries on top, but you can also do chocolate, peanut butter, and crushed nuts or seeds if you like! For the best texture and flavor, don't allow it to sit at room temperature for longer than an hour.

Storing Tips

  • Refrigerator: Protein cheesecakes must be stored in the refrigerator in an airtight container for up to 5 days. The mini cheesecakes may get slightly moist on top from the refrigeration. Take a paper towel and blot them gently before serving if this happens.
  • Freezer: I have not tried freezing healthy cheesecake, but I would not recommend it as the dairy products in this recipe generally don't freeze well.

Recipe FAQs

Can I make one large cheesecake?

I have not tried making one large cheesecake from this recipe, but it might work if you were to use a springform cheesecake pan. You will need to extend the baking time as it will take much longer to cook.

How do I know when my protein cheesecake is done?

The filling will firm up and will no longer be jiggly in the middle. You can test it by gently shaking the pan to watch for movement in the filling.

Protein cheesecake on a platter ready to eat.

More Low Calorie Dessert Recipes

  • Quinoa brownies cut into squares and stacked on top of each other.
    Fudgy Chocolate Quinoa Brownies
  • Healthy Berry Quinoa Crumble {GF, Vegan}
  • Avocado Key Lime Pie Bars! Made with a buttery gluten free oat crust that tastes like graham crackers and topped with creamy lime avocado Greek yogurt filling for an irresistible treat! A lighter twist on Key Lime Pie that's made with healthier ingredients and balanced in nutrition. Gluten Free + Low Calorie
    Avocado Key Lime Pie Bars {GF, Low Cal}
  • Skinny Strawberry Shortcake made nutritionally balanced with protein & oats in biscuit form for a portioned controlled dessert or snack. Perfect for those watching their weight or trying to lose weight. Gluten Free + Low Calorie
    Healthy Strawberry Shortcake

If you tried this protein cheesecake recipe or any other recipe on my website, please please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

Mini protein cheesecake bites are on a white platter and garnished with whipped cream and fresh fruit.

High Protein Cheesecake

Megan Olson
High Protein Low Calorie Cheesecake are a low fat treat made with Greek Yogurt, lower in sugar and delicious! 
5 from 2 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 30 minutes mins
Chill Time 4 hours hrs
Total Time 4 hours hrs 40 minutes mins
Course Dessert
Cuisine American
Servings 12 cheesecakes
Calories 122 kcal

Ingredients
 
 

  • 8 oz Light Cream Cheese room temperature
  • ¾ cup Non Fat Greek Yogurt room temperature
  • ⅓ cup Coconut Sugar
  • 1 Egg
  • 1 Egg Yolk
  • 1 teaspoon Vanilla Extract
  • 2 teaspoons Lemon Juice
  • 1 tablespoon Arrowroot Powder
  • 1 ½ cups Graham Cracker Crumbs about 10 sheets
  • 5 tablespoons Butter melted

Instructions
 

  • Preheat the oven to 350 F. Line 12 muffin cavities with cupcake liners.
  • Add the graham crackers to a food processor and process until they have the appearance of crumbs. Add the melted butter and pulse a few times to combine.
  • Divide the graham cracker crumbs among the 12 muffin cavities lining the bottom of each one. Press the crumbs firmly into the bottom of the cavity to form the crust.
  • Bake for 5 minutes in the heated oven. Remove the pan from the oven and let it cool while you prepare the filling.
  • Add the cream cheese and Greek yogurt to a large mixing bowl and beat with an electric mixer. Once smooth, add the sugar, lemon juice, vanilla extract, egg, egg yolk and arrowroot powder. Beat with an electric mixer on a low setting until smooth.
  • Divide the filling among the 12 muffin cavities, placing on top of the cooked crust. Bake for 18-20 minutes until the filling has set. It should not wiggle.
  • Remove from the oven and cool at room temperature for 30 minutes then chill for 4 hours in the refrigerator.
  • Remove from the refrigerator top with Reddi Whip and freshly sliced berries and blueberries and serve!

Notes

  • I recommend silicone muffin liners as the cheesecake will easily release. Paper doesn't work as well.
  • When the eggs, lemon juice, cream cheese and yogurt are at room-temperature this ensures your cheesecake is perfectly smooth and has the right texture. Using cold ingredients will increase the bake time and potentially they will turn out under baked.
  • Beat the filling just until the ingredients are combined otherwise the filling will be tough.
  • Remove the mini protein cheesecakes from the oven once the filling has set and is not jiggling. Over baked cheesecakes will not be as creamy and will be more sponge-like.
  • These low calorie cheesecakes are best made 24 hours in advance of serving. They require at least 4 hours of chilling but if they can set in the refrigerator overnight it's even better.

Nutrition

Serving: 1cheesecakeCalories: 122kcalCarbohydrates: 15gProtein: 4gFat: 5gSaturated Fat: 2gPolyunsaturated Fat: 0.3gMonounsaturated Fat: 2gTrans Fat: 0.003gCholesterol: 41mgSodium: 163mgPotassium: 99mgFiber: 0.4gSugar: 7gVitamin A: 157IUVitamin C: 0.3mgCalcium: 62mgIron: 1mg
Tried this Recipe? Let me know!Let us know how it was!

About Megan

Megan is a certified nutrition practitioner, author, freelance food photographer and fitness instructor living in Phoenix, Arizona. On her blog, Skinny Fitalicious she shares EASY, gluten free recipes for weight loss. Follow Megan on Facebook, Twitter, Pinterest and Instagram for the latest updates.

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    5 from 2 votes (1 rating without comment)

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  1. Melinda says

    May 18, 2025 at 2:33 pm

    Delicious! I made these for a party and they were a huge hit. Thank you!

    Reply

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