Healthy Treats

Healthy Apple Pie Cheesecake

Apple pie cheesecake is healthy and made with warm spices that remind you of fall. Perfect topped with vanilla ice cream or cool whip!

close up of a mini apple pie cheesecake surrounded by apples and cinnamon sticks

Fall has officially made its appearance. Last week we had one random 80°F day here in Madison, which was quickly followed by a drop down to the 50’s.

With all this cooler weather, I was feeling very inspired to make some fall-like desserts.

Instantly, apple pie came to mind. But I wanted to switch things up a bit and opted for apple pie cheesecake.

overhead shot of mini apple pie cheesecake surrounded by cinnamon sticks and fresh apples.

I went even further down the rabbit hole though, and decided mini apple pie cheesecakes would be even better!

My instincts were totally spot on, because these little bite-sized cheesecakes were just the right amount of creamy cheesecake and stunning apples. I definitely could have had more than one!

Making Apple Pie Cheesecake

The crust

I love a good graham cracker crust with cheesecake. The buttery crushed graham cracker with cool cream cheese is a match made in heaven.

But, if we’re going down a fall rabbit hole, I wanted to change things up slightly with the crust.

Enter the cinnamon graham cracker!

box of graham crackers with graham crackers next to it and fresh apples

Cinnamon plays a huge role in apple pie, so why not go all out with a crust to match? This was definitely a wise move!

The simplicity of the crust makes these cheesecakes even better. All you have to do is crush the graham crackers, mix with melted butter, and press into lined muffin tins.

cupcake pan lined with cupcake liners and filled with crushed graham crackers. A bowl with graham cracker mixture sitting next to it.

The cheesecake filling

Since we’re making a play on apple pie, I really wanted to spice up the cheesecake batter.

It’s best to start with room temperature, or well softened cream cheese. We’re looking for absolutely no lumps when we beat the cream cheese.

Add in some Greek yogurt for a tangy and extra creamy base to this cheesecake.

cupcake liners filled with cheesecake filling, sitting next to a bowl of chopped apples.

Then on to the spices!

Cinnamon is an obvious must when it comes to apple pie, but what other spices need to be invited to the party?

I went with nutmeg and cloves, for a sweet and rich aroma and full-bodied flavor in our apple pie cheesecake.

The apple pie topping

The other reason I was dying to make these apple pie cheesecakes wasn’t just because the weather turned chilly and the leaves are started to change colors.

cheesecakes topped with diced apples ready to be baked

No, I wanted to make these because I have an obsession with honeycrisp apples. The bonus was that our local grocery store was having a massive sale on this crisp, yet sweet apple.

It just seemed like fate.

The topping is pretty simple and consists of fresh apples, almond flour to bind, and pure maple syrup for sweetness.

How to enjoy apple pie cheesecake

Really, there’s no wrong way to enjoy these beauties.

Whether you opt for a side of cool vanilla ice cream, or a large dollop of cool whip, or even just eating them plain. You’re going to highly enjoy, and devour them!

overhead shot of mini apple pie cheesecake surrounded by cinnamon sticks and fresh apples.

All of the spices play so well together, and the apple topping just rounds out the mini cheesecakes. Enjoy these all throughout fall, but especially for Thanksgiving dessert.

Looking for more fall-inspired desserts? Check these out:

Apple Pie Snack Mix

Healthy Cherry Cheesecake

Healthier Pumpkin Lush

These mini apple pie cheesecakes are healthy and made in muffin tins. They have a cinnamon graham cracker crust, and are the perfect fall dessert, or Thanksgiving dessert. #thanksgiving #healthycheesecake #minidesserts #holidaydesserts #easycheesecakerecipe
Healthy Mini Apple Pie Cheesecakes
Prep Time
15 mins
Cook Time
50 mins
Total Time
1 hr 5 mins
Apple pie cheesecake is healthy and made with warm spices that remind you of fall. Perfect topped with vanilla ice cream or cool whip!
Course: Dessert
Cuisine: American
Keyword: apple pie, cheesecake, fall dessert, thanksgiving
Crust Ingredients:
  • 9 cinnamon graham crackers crushed {abt. 1 ½ cups}
  • 6 Tbsp. butter melted
Cheesecake Ingredients:
  • 8 oz cream cheese softened
  • 1 cup plain low fat Greek yogurt
  • 1 egg
  • cup coconut sugar
  • 1 ½ Tbsp. cinnamon
  • 1 tsp. ground cloves
  • 1 tsp. ground nutmeg
  • 1 tsp. vanilla
Apple Pie Topping Ingredients:
  • 2 medium honeycrisp apples peeled and diced {abt. 2 ½ cups}
  • cup pure maple syrup
  • 2 Tbsp. almond flour
  • 1 Tbsp. cinnamon
  • 1 tsp. vanilla
  1. Preheat oven to 350°F and line two muffin tins with 17 cupcake liners.
  2. In a small bowl, stir together the crushed graham crackers and melted butter.
  3. Press about 1 Tbsp. of crust into the bottom of each cupcake liner.
  4. Bake for 10 minutes until edges are lightly browned. Remove and let cool slightly.
  5. Meanwhile, in a medium-size bowl, beat the cream cheese until smooth. Add the Greek yogurt, and continue to beat until combined and smooth. Add the egg and beat until smooth.

  6. Add the coconut sugar, cinnamon, cloves, nutmeg and vanilla and beat until incorporated. Spoon the mixture into the cupcake liners, filling about ¾ full.
  7. In a separate medium-size bowl, stir together the apple pie topping ingredients. Spoon over the cheesecake batter.
  8. Bake for 38-40 minutes, until cheesecake is set. Remove and let cool.
  9. Cover and place in the refrigerator to chill for 5-8 hours.
  10. Enjoy with ice cream or cool whip topping.
Recipe Notes

Note: these mini cheesecakes freeze really well. Unwrap them from the cupcake liners and place in an airtight container in the freezer. When ready to eat, remove and let thaw for 1-2 hours. 

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