If you love cheesecake but don’t want to go through the hassle of making an entire cheesecake, these Mini Protein Cheesecakes are going to be your new favorite little treat!

They have everything you love about traditional cheesecake: a buttery graham cracker crust, a smooth and creamy filling, and that perfectly sweet, slightly tangy flavor. But we’re adding a little protein powder and Greek yogurt to give them a protein boost!

Each mini cheesecake has 172 calories and 7 grams of protein, making them a delicious treat that’s easy to fit into your day.

And one of my favorite things about this recipe? They’re baked in a regular muffin tin, so you get 12 individual cheesecakes without needing a springform pan or a water bath.

You can enjoy them plain, top them with fresh berries, drizzle them with chocolate, or add a little nut butter. They’re delicious just about any way you serve them!

These are also a great make-ahead dessert for holidays, parties, or when you want something sweet waiting in the refrigerator.

Why You’ll Love These Mini Protein Cheesecakes

• 7 grams of protein each. A little extra protein in a delicious dessert!
• Only 172 calories per cheesecake. Easy to portion and enjoy.
• Classic cheesecake flavor. Creamy filling with a buttery graham cracker crust.
• Made with Greek yogurt and protein powder. Two simple ways to add protein.
• No special cheesecake pan required. Just a regular 12-cup muffin tin.
• Perfect for making ahead. These taste even better after chilling in the refrigerator.
• Easy to customize. Add your favorite fruit, chocolate, or nut butter toppings.
• Great for sharing. Twelve individual cheesecakes make serving easy.

Ingredients You’ll Need

These mini cheesecakes use simple ingredients and come together in two easy layers.

For the Graham Cracker Crust

• Graham crackers: 10 full sheets, crushed into fine crumbs.
• Vanilla protein powder: ½ scoop (17g) to add a little extra protein to the crust.
• Butter: 5 tablespoons, melted, to hold the crust together and give it that classic buttery flavor.

For the Cheesecake Filling

• Reduced-fat cream cheese: 8 ounces of ⅓-less-fat cream cheese, softened to room temperature.
• Plain nonfat Greek yogurt: ¾ cup (170g), also at room temperature.
• Sugar: ⅓ cup for sweetness.
• Protein powder: 1 scoop (33g) of Clean Simple Eats Vanilla or Key Lime Pie protein powder.
• Vanilla extract: 1 teaspoon.
• Eggs: 1 whole egg and 1 egg white, both at room temperature.

I love that you can use either Vanilla or Key Lime Pie protein powder in this recipe. Vanilla gives you a more traditional cheesecake flavor, while Key Lime Pie adds a fun citrus-inspired twist!

Nutrition Information & Macros

Makes: 12 mini cheesecakes

Serving Size: 1 mini cheesecake

• Calories: 172
• Protein: 7g
• Carbohydrates: 12.1g
• Fat: 10.3g
• Fiber: 0.5g

Nutrition information is based on the ingredients listed and does not include optional toppings. Macros may vary depending on the protein powder and other brands used.

One Important Tip for Creamy Cheesecake

Use room-temperature ingredients!

This is probably the most important tip I can give you when making cheesecake.

Cold cream cheese can create lumps in the filling, and adding cold eggs or yogurt can make it harder to achieve a smooth, creamy consistency.

Before you begin, allow your cream cheese, Greek yogurt, egg, and egg white to come to room temperature.

You’ll get a smoother filling without having to overmix the batter.

And when it comes to cheesecake, a smooth filling makes all the difference!

One more baking tip: Don’t wait until the centers are completely firm before removing the cheesecakes from the oven. The edges should be set, but the centers can still have a slight jiggle. They’ll continue to firm up as they cool and chill in the refrigerator.

Vanilla vs. Key Lime Pie Protein Powder

One of the fun things about this recipe is that you can change the flavor simply by switching your protein powder.

Vanilla Protein Cheesecakes

Using vanilla protein powder gives these mini cheesecakes a classic cheesecake flavor.

They’re delicious plain or topped with strawberries, blueberries, raspberries, or a little chocolate.

Key Lime Pie Protein Cheesecakes

If you love citrus desserts, try Clean Simple Eats Key Lime Pie protein powder!

It adds a subtle key lime-inspired flavor that pairs beautifully with the tanginess of the cream cheese and Greek yogurt.

You could even top these with a little fresh lime zest for an extra pop of flavor.

Both options work great, so use whichever flavor you have on hand!

My Favorite Mini Cheesecake Toppings

These mini protein cheesecakes are delicious all on their own, but adding toppings is an easy way to make them feel extra special.

Here are a few ideas:

• Fresh strawberries: Sliced or diced strawberries are a classic cheesecake topping.
• Blueberries or raspberries: Perfect for adding a little natural sweetness.
• Chocolate drizzle: Melt a little chocolate and drizzle it over the top.
• Nut butter: A small drizzle of peanut butter or almond butter is delicious.
• Whipped cream: Add a little whipped cream just before serving.
• Fresh lime zest: Especially delicious with Key Lime Pie protein powder.
• Sugar-free fruit preserves: An easy way to add fruit flavor without making a separate topping.

If you’re making these for a party, you could set out a few different toppings and let everyone customize their own cheesecake!

Just remember that toppings are not included in the listed macros.

Why Use Greek Yogurt in Cheesecake?

Greek yogurt is one of my favorite ingredients to use in higher-protein recipes.

In these mini cheesecakes, it helps create a creamy filling while adding protein and a little tanginess.

Traditional cheesecake recipes often use a larger amount of cream cheese, sour cream, or heavy cream.

By combining reduced-fat cream cheese with nonfat Greek yogurt, we can keep that delicious cheesecake flavor while incorporating an additional source of protein.

The result is a creamy, satisfying dessert that still tastes like cheesecake!

Tips for Making the Best Mini Protein Cheesecakes

Use room-temperature ingredients. This helps prevent lumps and makes the filling easier to mix.

Don’t overmix after adding the eggs. Mix just until incorporated to avoid adding too much air.

Press the crust firmly. A tightly packed graham cracker crust holds together better when you remove the muffin liners.

Don’t overbake. The edges should be set, but a slight jiggle in the center is okay. The cheesecakes will firm up as they cool.

Let them chill completely. Refrigerating for at least 3 hours helps the filling set and gives you that classic cheesecake texture.

Wait to add toppings. For the freshest appearance and texture, add fruit, whipped cream, or other toppings right before serving.

Can You Make Mini Protein Cheesecakes Ahead of Time?

Absolutely! In fact, I think these are even better when you make them ahead.

Since cheesecake needs time to chill and set, this is the perfect dessert to prepare the day before you plan to serve it.

Simply bake the cheesecakes, allow them to cool, and refrigerate overnight.

When you’re ready to serve, remove them from the muffin tin, peel away the liners, and add your favorite toppings.

They’re perfect for holidays, birthday celebrations, family gatherings, or having a little something sweet prepared for the week.

How to Store Mini Protein Cheesecakes

Store the cheesecakes in an airtight container in the refrigerator for up to 4–5 days.

I recommend keeping them plain until you’re ready to eat them, especially if you’re planning to add fresh fruit or whipped cream.

For easy meal prep, you can store the cheesecakes individually or arrange them in a single layer in a larger airtight container.

Because these contain cream cheese, Greek yogurt, and eggs, they should be kept refrigerated.

Can You Freeze Mini Protein Cheesecakes?

Yes! These mini cheesecakes are a great freezer-friendly dessert.

Once they’ve completely cooled and chilled, place them in a freezer-safe container or wrap them individually.

Freeze for up to 2–3 months for best quality.

When you’re ready to enjoy one, thaw it overnight in the refrigerator.

I recommend freezing them without toppings and adding those after thawing.

The texture may change slightly after freezing, but they’ll still make a delicious treat.

Frequently Asked Questions

Can I use regular cream cheese?

Yes! Regular cream cheese should work, but it will change the calories and fat content of the recipe.

The listed macros are calculated using ⅓-less-fat cream cheese.

Can I use a different protein powder?

You can experiment with other whey protein powders, but the sweetness, flavor, and texture may vary.

I developed this recipe using Clean Simple Eats protein powder.

Can I use vanilla protein powder instead of Key Lime Pie?

Absolutely! Vanilla gives you a classic cheesecake flavor, while Key Lime Pie adds a citrus-inspired twist.

Do I need a water bath?

No! These mini cheesecakes are baked in a regular muffin tin, so there’s no need for a traditional cheesecake water bath.

Why did my mini cheesecakes crack?

Cracking can happen when cheesecake batter is overmixed or baked too long.

Try mixing the eggs in gently and removing the cheesecakes when the edges are set and the centers still have a slight jiggle.

And if a few crack? Don’t worry! A little fruit or whipped cream on top fixes everything.

How long do mini cheesecakes need to chill?

Refrigerate for at least 3 hours, although overnight is even better for the best texture.

Can I make these without the graham cracker crust?

You could experiment with a crustless version, but the baking time and nutrition information would change. I haven’t tested this exact recipe without the crust.

Are the toppings included in the macros?

No. The listed nutrition information includes the graham cracker crust and cheesecake filling, but not any optional toppings.

More High-Protein Desserts to Try

If you love finding ways to add a little protein to your favorite treats, be sure to check out some of our other Stay Fit Mom recipes!

• Protein Pudding
• PB&J Protein Bites
• Chocolate Baked Oats
• Cinnamon Sugar Donut Holes
• Pumpkin Chocolate Sheet Cake

Because hitting your protein goal doesn’t mean you have to give up dessert!

The Perfect Little Cheesecake Treat

These Mini Protein Cheesecakes are proof that you can enjoy a delicious homemade dessert while still being mindful of your nutrition goals.

With a buttery graham cracker crust, creamy cheesecake filling, and 7 grams of protein per serving, they’re a fun treat to make for yourself or share with family and friends.

I love that you can make a dozen at once, keep them in the refrigerator, and customize each one with your favorite toppings.

Whether you’re making them for a special occasion or just because you’re craving cheesecake, I think you’re going to love these!

If you try this recipe, be sure to leave a rating and comment below. I’d love to hear which protein powder flavor and toppings you used!