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Healthy Cheesecake Bites (Cheesecake Cupcakes)

These healthy cheesecake bites are a delicious and nutritious twist on classic mini cheesecakes. They’re made with protein-rich cottage cheese, flour, natural sweetener, and eggs.

The easy-to-follow instructions will show you how to make a fuss-free, perfect batch every time. It makes 12 cheesecake bites (a.k.a. cheesecake cupcakes) which are perfect for everyday desserts, breakfast, and snacks.

Overhead shot of the healthy cheesecake bites in cupcake liners. The cheesecake bites are sitting on a tea towel.

I love when delicious desserts double as a light and healthy snack, and these cheesecake bites are just that. You’ll make the cutest and most delicious cheesecake bites with a short list of simple ingredients.

They keep well in the fridge and freezer and are perfect to prep once and snack on throughout the week.

Baking crustless cheesecake batter in a muffin pan instead of a full-size pie pan yields PERFECT results every time!

Before we go further, I should add that these easy mini cheesecakes were tested with pressed, no-salt-added, 0.5% cottage cheese. Western brand cream cheese is my favorite here in Canada.

If you use a different brand of cream cheese, I’d love for you to drop a comment letting me know how it turned out!

A package of pressed cottage cheese called Western.

Why You’ll Love This Recipe

Here are six reasons why this recipe is a keeper:

  • These healthy cheesecake bites are the best personal desserts to pack for picnics and potlucks.
  • The flavor and customization possibilities are endless.
  • These cheesecake cupcakes are a hit wherever they’re served.
  • This easy recipe is perfect for beginners and turns out well every time.
  • These little cheesecakes store well, so you’ll have a healthy dessert or snack within reach whenever you’re craving something sweet.
  • They make a perfect healthy dessert the whole family can enjoy.

Cheesecake bites on a tea towel. Side view.

Ingredients & Equipment

Here is an overview of the ingredients and equipment you will need to make cheesecake bites with cottage cheese:

  • Cottage cheese – Pressed, no salt added 0.5% cottage cheese such as Western. It is a delicious and nutritious alternative to heavy cream cheese and sour cream.
  • Milk – Adds more moister to the cheesecake bites to keep them rich and soft while baking.
  • Flour – I like baking with whole spelt flour as it’s more nutrient-dense, but whole wheat flour or regular all-purpose white flour also works well in this recipe.
  • Natural sweetener – You can use coconut sugar, date sugar, maple syrup, honey, etc.
  • Vanilla – Use a quality pure vanilla extract to enhance the sweet cream-like flavors.
  • Eggs – Play a role in flavor, moisture, and keeping the cheesecake bites from falling apart.
  • Raisins & walnuts – For a pop of fruity flavor and some crunch. These ingredients are optional.
  • Recommended equipment – To make these mini cheesecakes, you’ll need a muffin tin or cupcake pan, muffin liners, and a high-speed blender or powerful food processor. It isn’t easy to mix pressed cottage cheese with the other ingredients by hand.

How To Make Healthy Cheesecake Bites

Here are the step-by-step instructions on how to make cheesecake bites:

  1. Blend the ingredients: Add the cottage cheese, milk, flour, sugar, vanilla extract, and eggs to the carafe of a high-speed blender or a powerful food processor, and blend until smooth and well combined.
  2. Mix in dried fruit and nuts: Transfer the batter to a large mixing bowl. Add the raisins and walnuts, and mix with a wooden spoon until combined. If you have a larger blender or food processor, you can mix everything in the equipment instead of transferring it to a bowl.
  3. Bake the batter: Divide the cheesecake mixture evenly in a baking cup-lined muffin pan. If you are using a silicon muffin pan, skip the cupcake liners and lightly brush it with melted coconut oil. Bake cheesecake bites until the edges appear set and the middle is still soft and jiggly (25 minutes).
  4. Let cool: At this point, the cheesecake bites will be very delicate, so carefully remove the pan from the oven and avoid fussing with them or they will fall apart. Instead, let them cool in the muffin pan for 30 to 40 minutes, then carefully transfer them to a wire rack to finish cooling before storing them in the fridge.

Cheesecake cupcakes in a glass container.

Recipe Tips

As a rule of thumb, set refrigerated baking ingredients (cottage cheese, milk, and eggs) on the counter for 15-20 minutes or until they reach room temperature before baking.

To make mini cheesecake bites with a crust, moisten crushed graham crackers (or Oreo or any crunchy cookie) with melted butter, and then press a thin layer of the mixture into the bottom of the cupcake liner.


You can make this delicious treat even better with these toppings and mix-ins:

  • Sweet syrups – Drizzle chocolate sauce, strawberry syrup, or raspberry sauce over the top of each bite.
  • Compotes – Garnish with a spoonful of raspberry, blackberry, or blueberry compote.
  • Fresh fruit – Serve with sliced bananas, apples, oranges, papaya, kiwi, and/or a mixture of fresh berries. 
  • Dried fruit – If you aren’t feeling the raisins, swap in your favorite dried fruit (chopped pineapple, mango, dates, etc.).
  • Nuts – Instead of walnuts, try pecans, almonds, macadamia nuts, or pistachios.
  • Fruit spreads – After dividing the batter evenly in the muffin tin, drop about a 1/2 tablespoon of lemon curd or any flavor fruit jam, preserves, or marmalade into the center. Use a toothpick to swirl it into the batter, then bake.

Storing & Freezing

Storing: Once baked, these mini cheesecakes can be kept in the refrigerator for 3-4 days.

Be sure to store them in an airtight glass container so they don’t absorb any lingering odors in the fridge.

Freezing: The cheesecake bites freeze and thaw out beautifully. Simply wrap each bite tightly in plastic wrap, and then freeze in a heavy-duty freezer bag or container for up to 2 months.

They’re best thawed in the fridge overnight, but if you’re in a hurry, you can pop one into the microwave for 15-20 seconds.

Cheesecake cupcakes on a tea towel.

Frequently Asked Questions

Here are a few related questions about cheesecake bites:

Do cheesecake bites need to be refrigerated?

Yes. Baked cheesecake bites must be stored in the fridge because they contain perishable dairy ingredients and eggs.

How long are homemade cheesecake bites good for?

If kept in an airtight container in the fridge, these cheesecake bites will last 3-4 days, but they’ll most likely be gobbled up long before then.

Can you make cheesecake bites with cottage cheese?

Yes, it’s possible to use cottage cheese combined with whole milk instead of sour cream or cream cheese to make cheesecake bites. This recipe will show you how!

However, the curds will give the batter a grainy texture, so you’ll need to blend the mixture with a food processor or high-speed blender until smooth.

More Healthy Dessert Recipes

Here are a few other healthy dessert recipes for you to check out:

Sweet Cheese Cups

Healthy Cheesecake Bites

Yield: 12 cupcakes
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

These easy mini cheesecake bites are very easy and quick to make. They are great as a snack or dessert and keep well in the fridge for several days. Perfect for meal prep.


  • 500 gr ( about 2 to 2 1/4 cups) pressed no salt added 0.5% cottage cheese such as Western
  • 1/4 cup milk
  • 2 Tbsp whole spelt flour ( whole wheat or regular all-purpose white flour also works)
  • 1 Tbsp coconut sugar or other natural sweeteners
  • 1 tsp vanilla extract
  • 3 eggs
  • 1/2 cup raisins (optional)
  • 1/2 cup walnut pieces (optional)

You will also need:

  • baking cups
  • muffin pan


  1. Preheat the oven to 350F.
  2. Place the cottage cheese, milk, flour, sugar, vanilla extract, and eggs into a food processor. **See the Notes.
  3. Blend the ingredients until smooth and well combined.
  4. Transfer the mixture into another bowl (if your blender or food processor bowl is big enough, you don't need to do that) and add the raisins and walnut pieces. Mix using a wooden spoon until just combined.
  5. Place the baking cups into a muffin pan. Spoon the mixture into the baking cups making sure it's divided evenly. Bake in the preheated oven for 25 minutes.
  6. Once you take the muffin pan out of the oven, the cheesecake cupcakes will be very soft. Resist the urge to touch them because they will fall apart. Leave them in the muffin pan for about 40 minutes. Then carefully transfer to a cookie rack to cool completely.
  7. Serve cold or warm.
  8. The cupcakes keep well in the fridge for up to 3 days.


  1. You would really need a good blender or food processor as it's very difficult to mix pressed cottage cheese with the other ingredients by hand.
  2. You don't need cupcake liners if you are using a silicon muffin pan. Just lightly brush it with melted coconut oil before adding the cupcake batter.
  3. Nutrition information is a rough estimate for 1 of 12 cupcakes made with raisins and walnuts.
Nutrition Information
Yield 12 Serving Size 1 cupcake
Amount Per Serving Calories 96Total Fat 3.8gSaturated Fat 1.2gTrans Fat 0gUnsaturated Fat 1.7gCholesterol 47.6mgSodium 170.5mgCarbohydrates 9gFiber 0.5gSugar 6.2gProtein 6.2g

Nutrition facts provided on this website are an estimate and not guaranteed to be accurate. Please see a qualified health care provider for personalized diet advice and make sure that each of the ingredients is allowed in your diet.

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