Name: Mini Protein Pumpkin Cheesecakes
Prep time: 10 min
Cook time: 20 min
Total time: 30 min
Ingredients: 1 ½ cups graham cracker crumbs (gluten-free if needed (about 10 sheets)); 5 tbsp melted salted butter; 8 oz cream cheese (room temperature, regular or low fat if desired); ⅔ cup plain 0% Greek yogurt (room temperature); ⅓ cup canned pumpkin puree; ⅓ cup granulated sugar; 1 large egg + 1 yolk; 1 tsp vanilla extract; 1 tbsp pumpkin pie spice (yes 1 Tablespoon); ⅓ cup vanilla protein powder (or pumpkin spice)

These mini protein pumpkin cheesecakes are the perfect healthy, bite-sized dessert with over 7 grams of protein per serving! They have a homemade buttery graham cracker crust and are made with Greek yogurt, light cream cheese, and protein powder.

mini protein pumpkin cheesecakes with whipped cream on top

Mini pumpkin cheesecakes made with Greek yogurt and protein powder

Since these mini protein cheesecakes were such a hit (they are ranked #1 on Google), I decided I needed to add a pumpkin spices version for you since it's officially Fall. So say hello to the best, lightened-up, healthier mini pumpkin protein cheesecake bites. They are truly incredible.

These mini protein pumpkin cheesecakes are made with fat-free 0% Greek yogurt, reduced-fat cream cheese, eggs, vanilla extract, and protein powder. Plus, they have a homemade, two-ingredient graham crack crust that melts in your mouth.

Each little pumpkin cheesecake bite is light, smooth, and creamy! But the best part about them is that you can't tell they are healthy since they taste like a classic pumpkin-spiced cheesecake and have the same texture.

These high-protein pumpkin pie cheesecake bites are everything you want in a dessert. Seriously, everyone will love this recipe. They are simply perfect for Fall and Winter; your kids will love them, and they are ideal for Thanksgiving. I cannot wait to hear what you think!

Why you'll love this healthy dessert recipe:

High Protein: These mini pumpkin cheesecakes have a hidden protein boost with Greek yogurt and protein powder.
Easy to Make: Simple recipe for bakers of all levels.
Delicious Flavor: Rich, creamy pumpkin taste with warm spices.
Healthier Ingredients: We use a mix of Greek yogurt and light cream cheese to lighten these cheesecake bites up.
Mini: I love mini, bite-sized desserts!
Low-Fat Option: They can be made with low-fat cream cheese and 0% Greek yogurt.
Gluten-Free Option: Accommodates gluten-free diets with the right graham crackers.
Make-Ahead: Prepare in advance, and chill until serving.
Holiday Favorite: Perfect for fall and holiday gatherings.
Topping Options: Versatile with various toppings like whipped cream, drizzle of caramel, or chopped nuts.
Try these classic protein mini cheesecakes or this gluten-free pumpkin cheesecake next!

bite shot of a mini protein pumpkin cheesecakes to show soft, creamy middle

Ingredients needed

These mini protein pumpkin cheesecake bites are the perfect healthier dessert everyone will love. They're warmly spiced with pumpkin pie spice, soft and creamy, lightened up with Greek yogurt, and high protein. Here is a list of all the ingredients you will need to make these pumpkin cheesecake bites. Scroll to the recipe card at the bottom to see the exact measurements.

Protein Cheesecake Filling:

Cream Cheese: Provides a creamy, tangy cheesecake texture. Use regular, light, or low-fat "Neufchatel" cream cheese.
Greek Yogurt: Adds creaminess and boosts protein. Greek yogurt replaces 1 bar of cream cheese in this recipe to make these cheesecakes lighter, higher in protein, and healthier.
Canned Pumpkin Puree: Infuses the dessert with a delightful pumpkin flavor.
Granulated Sugar: Sweetens the cheesecake mixture - you only need a dash.
Egg and Egg Yolk: Bind the ingredients and provide structure. The egg york helps with the creamy texture, too!
Vanilla Extract: Enhances the overall flavor.
Pumpkin Pie Spice: Imparts warm, seasonal spices to the dessert. You can use homemade pumpkin pie spice or store-bought.
Protein Powder: Use vanilla or pumpkin pie spiced protein powder. I use whey, but pea protein works too to boost the protein content without compromising taste.
Whipped Cream (Topping): Adds a light and airy finish to the cheesecakes.

Gluten-Free Graham Cracker Crust:

Graham Crackers: They create a crunchy, sweet base for these mini pumpkin protein cheesecake bites.
Melted Butter: Binds the crumbs for the crust and adds richness. I used salted, but you can use unsalted and add a pinch of salt.

Kitchen tools needed

You only need a few kitchen utensils to make these lightened-up mini pumpkin protein cheesecakes. Here is a list:

Two Mixing Bowls
Electric Handheld Mixer
Cupcake Tin
Cupcake Liners
Measuring Tools: ½ teaspoon, 1 teaspoon, 1 Tablespoon, ¼ cup, ⅓ cup, ½ cup, and 1 cup.

all ingredients in mini protein pumpkin cheesecakes in small bowls with labels

How to make mini pumpkin protein cheesecakes

Homemade mini pumpkin protein cheesecakes are so easy to make. Any level baker can make them! Simply prepare the homemade crust, then add your filling and bake. Here are easy step-by-step instructions with pictures so any level baker can make this simple recipe.

Step 1:

First, preheat your oven to 325°F (163°C) and line a cupcake tin with 12 liners.

Step 2:

Then, make the crust. Place graham crackers in a food processor and pulse until they become crumbs. Alternatively, you can place them in a plastic bag and crush them with a rolling pin. Then, combine the crumbs with the melted butter in a large mixing bowl.

Step 3:

Now, divide the crumb mixture evenly among the muffin liners, using about 1.5 tablespoons each. Use your fingers to flatten and pack the crumbs firmly into the bottom of the liners.

making homemade graham cracker crust with melted butter and graham cracker crumbs

using a spoon to press down the graham cracker crust into the muffin cups

graham cracker crumbs in 12 muffin liners

Step 4:

Bake the crusts for 5 - 6 minutes. Remove them from the oven and let them cool for 5 - 10 minutes while you prepare the filling.

Step 5:

While the crusts cool, in a large mixing bowl, beat the cream cheese with a handheld electric mixer until it becomes smooth. Alternatively, you can use a stand mixer on medium.

whisking healthy, high-protein pumpkin cheesecake batter in a mixing bowl

Step 6:

Add the Greek yogurt, egg, egg yolk, vanilla extract, pumpkin puree, granulated sugar, pumpkin pie spice, and protein powder to the cream cheese. Mix on the lowest setting until smooth for about 30 - 60 seconds. TIP: be careful not to overbeat.

Step 7:

Then, divide the cheesecake filling evenly among the muffin liners. TIP: don't overfill them.

Step 8:

Finally, bake for 20 - 25 minutes or until the filling has set and no longer jiggles or appears wet.
Allow the mini cheesecakes to cool for 30 minutes at room temperature before transferring them to the refrigerator. Chill for at least 3 hours in the fridge.

Before serving, top each mini cheesecake with whipped cream. Enjoy!

unbaked mini pumpkin cheesecakes batter on top of the graham crack crust in a muffin tin

baked mini pumpkin protein cheesecakes in a muffin tin

Expert recipe tips

Room Temperature Ingredients: Ensure the cream cheese and Greek yogurt are at room temperature. This ensures a smoother and creamier cheesecake batter without lumps.
Select Quality Protein Powder: When choosing a protein powder for this recipe, opt for a high-quality product that complements the flavor. Use vanilla or pumpkin pie protein powder, not chocolate or another store, overpowering flavor.
Do Not Overmix: When mixing the cheesecake batter, avoid overmixing. Overmixing can lead to a dense texture. Mix only until the ingredients are combined and smooth.
Leave time for the Cheesecakes Cool and Set: It's crucial to refrigerate the mini pumpkin cheesecakes for at least 3 hours before serving. If you skip this step, they may be warm and too runny. For optimal results, prepare them a day in advance and let them chill overnight.
No Water Bath needed: This recipe is so easy that you don't need a water bath!
Ingredient Substitutions: I left a long list in the section below, but you can substitute Greek yogurt, light cream cheese, butter, graham crackers, and vanilla protein powder if needed.
Variations: Feel free to customize your cheesecakes with different toppings like caramel sauce, chocolate shavings, or chopped nuts for added texture and flavor.

greek yogurt and protein powder pumpkin cheesecakes

Ingredient substitutions

I bake a lot, so here is a list of the best ingredient substitutions for these mini pumpkin protein cheesecakes. I only recommend swapping out one or two, so the original recipe does not change too much.

Graham Crackers: Substitute with crushed digestive biscuits, Biscoff cookies, or a gluten-free alternative if needed.
Salted Butter: You can use unsalted butter and add a pinch of salt to control the saltiness, or use melted coconut oil.
Cream Cheese: Opt for regular or low-fat cream cheese based on your preference.
Greek Yogurt: Sour cream or blended cottage cheese can replace Greek yogurt.
Canned Pumpkin Puree: Make your own pumpkin puree from fresh pumpkin if you have it; don't use pumpkin pie filling!
Pumpkin Pie Spice: Create your own spice blend with cinnamon, nutmeg, allspice, and cloves.
Protein Powder: Choose a protein powder flavor that complements the cheesecake, such as vanilla or pumpkin pie. You can use Pea or Whey.

Are they healthy?

These high-protein mini pumpkin cheesecakes are healthy for many reasons. Here are a few:

Added Greek Yogurt. We incorporate 0% Greek yogurt to lighten up these mini pumpkin cheesecakes, making them a healthier choice and boosting protein content. Traditional recipes often use full-fat sour cream or cream cheese.
Reduced Fat: These pumpkin cheesecake bites have a lower fat content compared to traditional recipes because we utilize fat-free 0% Greek yogurt and light cream cheese.
High Protein. These bite-sized cheesecakes pack a punch with 7 grams of protein per mini cheesecake, making them a protein-rich snack.
Gluten-Free. Use gluten-free graham crackers to make the mini cheesecakes gluten-free!
Real Pumpkin: We actually add real pumpkin puree to these mini cheesecakes!

healthy protein pumpkin cheesecakes bites

Frequently Asked Questions

What's the best type of protein powder to use?

The best protein powder for this recipe is a mild flavor, like vanilla or pumpkin, to complement the pumpkin cheesecakes without overpowering them.

Can I make them gluten-free?

To make these mini protein pumpkin cheesecakes gluten-free, use gluten-free graham crackers for the crust.

Do I have to use a water bath?

No, a water bath is unnecessary for these mini pumpkin protein cheesecakes.

How many grams of protein are in these mini cheesecakes?

These mini cheesecakes contain 7 grams of protein per serving.

What's the best substitute for the graham crackers?

You can use digestive biscuits or Biscoff cookies instead of graham crackers for the crust.

Should cheesecake be eaten warm or cold?

Cheesecake is traditionally eaten cold, as it's best enjoyed after being chilled in the refrigerator for a few hours or overnight to set and develop its rich, creamy texture and flavor.

Can you make cheesecake ahead of time?

You can certainly make these mini pumpkin protein cheesecakes ahead of time. Feel free to make them the day before and store them in the fridge before serving.

Can you freeze mini cheesecakes?

After your pumpkin protein cheesecakes are set in the fridge, transfer them to freeze-safe bags or containers and freeze them for up to 3 months. When you are ready to enjoy them, let them thaw in the fridge for a few hours, then at room temperature for 10 minutes before serving.

How to store protein cheesecake:

For best results, store leftovers in an airtight container in the refrigerator for up to 5 days.

healthy mini protein pumpkin cheesecake bite

If you love this recipe, try these high-protein desserts next!

Did you make this recipe?

If you make this recipe, be sure to comment and rate it down below. Also, don't forget to tag me @healthfulblondie on Instagram and use the hashtag #healthfulblondie so I can see your delicious creation and share it with my followers!

📖 Recipe

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Mini Protein Pumpkin Cheesecakes