Rich, decadent mini chocolate cheesecakes with a gluten-free oreo crust and a chocolate ganache topping. This lighter, healthier, protein cheesecake recipe has the same delicious cheesecake flavor, but is made with cottage cheese instead of cream cheese! Packed with protein, and absolutely delicious, this is the perfect gluten-free cheesecake even your kids will love! 

a close up shot of a mini protein cheesecake muffing topped with whipped cream and a raspberry

What Makes This Recipe Great

Who says protein powder is only good for smoothies? If you’ve been around my site lately, you know that I am loving trying out new ways to sneak protein powder into tasty, feel-good foods (see my Vegan Baked Oats, Protein Mug Cake, and Protein Pancakes!)! The result? Protein-packed dishes that taste amazing, and fill you up! Next up, protein cheesecake! 

This chocolate protein cheesecake recipe features decadent, delicious mini cheesecakes with all of the same flavors of classic cheesecake, but healthier! Complete with a gluten-free oreo crust and an optional chocolate ganache topping, these tiny morsels are a gift that keeps on giving! 

Even better? They’re a gluten-free, kid-friendly, and high-protein dessert (or snack!) that is pretty much guilt-free. Prepped and baked in 30 minutes, then chilled for maximum deliciousness. Let’s get baking!

Ingredient Notes

recipe ingredients in nesting bowls and labeled

Gluten-Free Crust

  • Gluten-Free Sandwich Cookies: Gluten Free Oreos or Kinnikinnick brands work well.
  • Ghee: You can also use melted vegan butter. 

Cheesecake Filling

  • Cottage cheese: I used 1% milkfat cottage cheese instead of cream cheese to keep these light, and packed with protein! I have yet to find a dairy free cottage cheese, but Good Culture makes a great lactose free version!
  • Eggs
  • Coconut sugar
  • Vanilla extract
  • ​​Protein powder: I used Be Well By Kelly Vanilla. You can use your favorite protein powder!
  • Arrowroot powder: You can swap this for tapioca starch if that’s what you have on hand. 
  • Dark chocolate chips: Enjoy Life makes my favorite gluten-free chocolate chips. Another great brand is Hu. 
  • Almond milk: You can also use coconut milk if preferred. 

Chocolate Ganache Topping (Optional)

  • Dark chocolate chips
  • Almond milk

Recipe Step by Step

numbered, step by step photos showing how to make this recipe
additional step by step photos showing how to add the batter to a muffin tin
  1. Preheat oven to 375.
  2. Add the cookies and butter to a food processor and pulse until a crumb-like mixture is formed. It should resemble sand. You can also smash the cookies (in a plastic bag) with a meat tenderizer and stir in the butter.
  3. Add 12 muffin liners to the pan. Spoon an equal amount of the mixture into each cup, then press down using your fingers to form the crusts. Bake for 7 mins.
  4. Meanwhile, add the cottage cheese, eggs, coconut sugar, vanilla, protein powder, and arrowroot powder to a blender or food processor. Blend for 1 minute until smooth. You may need to scrape down the sides/ use a long spoon to help stir halfway through.  Add eggs one at a time and mix on low speed for 1 minute to get air bubbles out. 
  5. Combine chocolate chips and almond milk in a microwave-safe dish and microwave in 30-second increments until melted and smooth. Pour into the blender and continue blending on low for 1 minute. Pour the mixture evenly into muffin tins on top of the crusts and bake for an additional 20-22 mins until the tops are firm and starting to crack. 
  6. ​​Let them cool completely before removing them. Chill in the fridge for 2-3 hours (or overnight). Top your protein cheesecake with optional ganache topping (make this by melting the chocolate chips and almond milk together in the microwave or over a double boiler), whipped cream, and berries. Enjoy!
five mini protein cheesecakes topped with whipped cream and a raspberry

Mary’s Tips & Tricks

  • Depending on your lifestyle and allergies, you can use vegan, gluten-free protein powder, or whey protein powder. There are a ton of options out there!
  • You can also use full-fat cottage cheese instead of 1% if preferred. 
  • If you want to make these chocolate peanut butter protein cheesecakes, feel free to add a couple of tablespoons of peanut butter to the batter. 

Serving Tips

  • Let them cool completely, then chill in the fridge for 2-3 hours (or overnight). 
  • Top with optional ganache topping (make this by melting the chocolate chips and almond milk together in the microwave or over a double boiler), whipped cream, and berries. 
  • Serve cold and enjoy!

Storage Tips

  • Store in an airtight container in the refrigerator for up to 5 days. 
  • To freeze, wrap the protein cheesecakes tightly in plastic wrap and store them in a freezer-safe container. Thaw in the refrigerator or at room temperature for about an hour and serve. 
a bit taken out of a chocolate cheesecake muffin to show the middle

Recipe FAQs

Are protein desserts good?

I sure think so! So many baked goods can be full of just empty calories, sugar, and carbs. They can leave you feeling kind of icky, and also not filled up so you want more and more. Adding protein powder to your desserts gives them more nutrients to keep you fuller for longer and not feel like you’re wasting calories on food that isn’t nutritious! 

Is gluten free cheesecake a good source of protein?

Traditional cheese usually uses full-fat cream cheese which has protein, but not as much as cottage cheese. There is also a ton of added sugar in the crust and the filling. This protein cheesecake recipe adds protein powder to give it an even higher protein content and makes some healthy swaps to make them still delicious, just a little lighter. 

More Healthy Dessert Recipes…

Healthy Apple Crumble

Paleo Lemon Bars

Dairy-Free Key Lime Pie Bars

Paleo Chocolate Chip Banana Bread Muffins

Vegan Berry Crisp

Love this recipe? Please leave a 5-star 🌟🌟🌟🌟🌟 rating in the recipe card below & a review in the comments section. Or, follow me on Facebook, Pinterest or Instagram today!

chocolate protein cheesecake with whipped cream and raspberries on top
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Easy Chocolate Protein Cheesecake Recipe

Yield: 12 cheesecakes
Prep Time: 15 mins
Cook Time: 32 mins
Chilling time: 2 hrs
Total Time: 2 hrs 47 mins
This lighter, healthier, protein cheesecake recipe has a gluten-free Oreo crust, a chocolate ganache topping, and a protein-packed cheesecake filling!
4.89 from 9 votes
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Ingredients

Crust

  • 18 gluten free chocolate sandwich cookies, Gluten Free Oreos or Kinnikinnick brand work well
  • 4 tbsp ghee, or butter

Filling

Optional Chocolate Ganache Topping

Equipment

Instructions
 

  • Preheat oven to 375.
  • Add the cookies and butter into a food processor and pulse until a crumb-like mixture is formed. It should resemble sand. You can also smash the cookies (in a plastic bag) with a meat tenderizer and stir in the butter.
  • Add 12 muffin liners to the pan. Spoon an equal amount of the mixture into each cup, then press down using your fingers. Bake for 7 mins.
  • Meanwhile, add the cottage cheese, coconut sugar, vanilla, protein powder, and arrowroot powder to a blender or food processor. Blend for 1 minute until smooth. You may need to scrape down the sides/ use a long spoon to help stir halfway through. Add eggs one at a time and mix on low speed for 1 minute to get air bubbles out.
  • Combine chocolate chips and almond milk in a microwave safe dish and microwave in 30 second increments until melted and smooth. Pour into the blender and continue blending on low for 1 minute. Pour the mixture evenly into muffin tins on top of the crusts and bake for an additional 20-22 mins until the tops are firm and starting to crack.
  • Let them cool completely before removing. Chill in the fridge 2-3 hours (or overnight). top with optional ganache topping (make this by melting the chocolate chips and almond milk together in the microwave or over a double boiler), whipped cream, and berries. Enjoy!

Notes

Mary’s Tips & Tricks

  • Depending on your lifestyle and allergies, you can use vegan, gluten-free protein powder, or whey protein powder. There are a ton of options out there!
  • You can also use full-fat cottage cheese instead of 1% if preferred. 
  • If you want to make these chocolate peanut butter protein cheesecakes, feel free to add a couple of tablespoons of peanut butter to the batter. 

Serving Tips

  • Let them cool completely, then chill in the fridge for 2-3 hours (or overnight). 
  • Top the protein cheesecake with optional ganache topping (make this by melting the chocolate chips and almond milk together in the microwave or over a double boiler), whipped cream, and berries. 
  • Serve cold and enjoy!

Storage Tips

  • Store in an airtight container in the refrigerator for up to 5 days. 
  • To freeze, wrap the protein cheesecakes tightly in plastic wrap and store them in a freezer-safe container. Thaw in the refrigerator or at room temperature for about an hour and serve. 

Nutrition

Serving: 1cheesecake, Calories: 350kcal, Carbohydrates: 37g, Protein: 9g, Fat: 19g, Saturated Fat: 12g, Polyunsaturated Fat: 0.5g, Monounsaturated Fat: 2g, Trans Fat: 0.003g, Cholesterol: 50mg, Sodium: 241mg, Potassium: 197mg, Fiber: 2g, Sugar: 22g, Vitamin A: 97IU, Vitamin C: 0.1mg, Calcium: 112mg, Iron: 1mg
Course: Dessert
Cuisine: American
Calories: 350
Author: Mary Smith