Mini Apple Pie Cheesecakes Recipe with Cottage Cheese

When you combine cozy apple pie flavors with creamy cheesecake and a protein boost, you get these mini apple pie cheesecakes! They are the perfect fall-inspired treat with 9 grams of protein each. They’re bite-sized, portable, and secretly packed with cottage cheese and protein powder for a nutritious twist that boosts your protein while tasting indulgent. Whether you’re meal prepping snacks for the week, planning a fall gathering, or just want a sweet bite after dinner, these little cheesecakes check all the boxes.

Mini Apple Pie Cheesecakes Recipe with Cottage Cheese

Each bite of these mini apple pie cheesecakes feels like a hug on a crisp fall day. The tender cinnamon apples bring that nostalgic apple-pie flavor, the cheesecake layer is smooth and creamy thanks to protein-rich cottage cheese, and the almond butter-maple drizzle ties it all together with just the right touch of nutty sweetness.

They taste like dessert, but with a nourishing twist that makes them feel good to eat any time of day!

What makes these little cheesecakes extra special is that they skip the heavy crust and instead focus on wholesome ingredients.

The cottage cheese, Greek yogurt, and protein powder all work together to create a filling, satisfying treat that won’t leave you with a sugar crash.

I’ve been baking these on repeat for my family this season, and they disappear almost as quickly as I make them.

Sweet, creamy, and comforting, but also nourishing – these mini cheesecakes really do it all. I can’t wait for you to bake up a batch and enjoy them, too!

Why you’ll love these mini apple cheesecakes

Protein-packed indulgence – Unlike traditional cheesecakes, these are made with cottage cheese (instead of cream cheese and sour cream) and protein powder for a dessert that doubles as a nourishing snack. It’s the perfect dessert that helps you meet your protein goal!

Perfectly portioned – Since they’re baked in a muffin tin, you get a satisfying bite of cheesecake and apple pie without overindulging.

All the cozy vibes – Cinnamon apples + creamy cheesecake = fall comfort in every bite.

Meal-prep friendly – These hold up beautifully in the fridge, making them ideal for prepping ahead so you can enjoy leftover cheesecake all week long!

Ingredients you’ll need for apple pie cheesecake bites

Scroll down to view the full recipe card below for the full cheesecake ingredients list, nutrition facts, and step-by-step instructions.

• Cottage cheese – Blended smooth for creaminess + protein.
• Egg – Helps bind the cheesecakes.
• Plain Greek yogurt – Adds tang and extra protein.
• Natural cane sugar – Just enough sweetness without overpowering.
• Almond butter – Brings richness and healthy fats.
• Vanilla extract – For that classic cheesecake flavor.
• Vanilla protein powder – For a high-protein boost.
• Apples
• Cinnamon – Cozy, warming spice.
• Maple syrup
• Coconut oil

How to make this mini apple cheesecake recipe

Step 1: Preheat oven to 350 degrees F. Lightly oil silicone muffin molds or a muffin pan with silicone liners (this recipe makes 7 mini cheesecakes).

Step 2: Add cottage cheese, egg, Greek yogurt, sugar, almond butter, vanilla, and protein powder to a blender. Blend until completely smooth.

Step 3: Pour the cheesecake batter into each muffin cup and bake cheesecake bites for 35–40 minutes, until the cheesecakes are set in the middle. Let them cool fully to room temperature before topping.

Step 4: In a skillet, cook diced apples with cinnamon and water over medium heat. Stir often, adding splashes of water as needed to prevent sticking, until apples are softened and smell like apple pie filling.

Step 5: In a small bowl, stir together almond butter, maple syrup, and melted coconut oil until smooth and pourable for your nutty caramel sauce alternative.

Step 6: Add a spoonful of apple pie topping and finish with a drizzle of almond butter sauce on the top of the cheesecakes.

Watch me make the perfect fall dessert

The full how to video can be watched below, or on my YouTube channel!

Storage & Meal Prep

These mini apple pie cheesecakes store beautifully, which makes them such a great option for meal prep or make-ahead desserts.

In the refrigerator, you can keep them in an airtight container for up to five days, and they’ll stay fresh and creamy.

If you’d like to save some for later, they also freeze really well. Just wrap each cheesecake individually in plastic wrap, pop them into a freezer-safe bag or container, and they’ll keep for up to two months.

When you’re ready to enjoy one, simply thaw it overnight in the fridge, and it will taste just as delicious as the day you baked them.

For the best texture, I recommend storing the apple topping and almond butter drizzle separately until serving.

That way, the cheesecakes stay firm, and you’ll get the perfect balance of creamy cheesecake filling, warm spiced apples, and nutty drizzle right before you dig in and enjoy it!

Serving ideas

These little cheesecakes are delicious on their own, but here are some fun ways to serve them:

• Add a dollop of whipped cream or Greek yogurt on top of the apple filling.
• Turn them into mini caramel apple cheesecakes with a generous caramel sauce drizzle
• Sprinkle with crushed walnuts, pecans, or crushed graham crackers for crunch.
• Pair with a cup of chai hot cocoa, or coffee for the ultimate cozy afternoon snack.
• Make them extra dessert-worthy with a scoop of vanilla ice cream on the side.

Nutrition benefits

Let’s talk about why these mini apple pie cheesecakes are more than just a treat:

• Cottage cheese brings protein, calcium, and probiotics for gut health.
• Greek yogurt adds extra protein and creaminess without needing heavy cream.
• Protein powder ensures you get a steady, filling boost – making these a great post-workout snack.
• Apples + cinnamon bring fiber, antioxidants, and natural sweetness.
• Almond butter + coconut oil provide healthy fats that keep you satisfied.

All of this means you get dessert vibes without the sugar crash. Win-win!

Substitutions, optional variations & dietary adjustments

Below you’ll find a list of substitutions that will work well in this apple cinnamon cheesecake recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Cottage cheese and Greek yogurt – These two higher-protein swaps replace the traditional cream cheese and sour cream. You can also swap those in if you don’t have cottage cheese or Greek yogurt available.

Protein powder – Swap vanilla for unflavored or cinnamon protein powder for a fun twist.

Cane sugar – Use coconut sugar, maple syrup, or honey instead of cane sugar.

Nut butter – Try peanut butter or cashew butter for a different flavor in the drizzle.

Apples – Use Granny Smith for tartness or Honeycrisp for natural sweetness. You could also swap pears or peaches or a different fruity twist!

More apple recipes you’ll love

• Apple crisp without oats
• Apple pie protein shake
• Apple pie overnight oats

If you try this great dessert recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather