Mini Caramel Apple Cheesecakes

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These mini caramel apple cheesecakes are perfect for your next fall gathering! Buttery graham cracker crusts are baked with a layer of caramel sauce and a creamy cream cheese filling, then topped with tender spiced apples and caramel sauce to make the perfect single-serve desserts!

Easy Mini Caramel Apple Cheesecakes

You are in for a fall treat! These cute mini cheesecakes are bursting with caramel apple flavor and are the perfect dessert to bring to your next gathering. They are made with a classic graham cracker crust, a layer of my favorite caramel sauce and rich and creamy vanilla cheesecake. They are then topped with cubed apples that have been cooked in cinnamon and nutmeg and drizzled with even more caramel sauce. You will fall in love with how tasty these are!

I love that these mini cheesecakes are so much quicker to make than a traditional cheesecake and are much more hassle-free. The inspiration came from my Salted Caramel Cheesecake, which also has caramel sauce in the filling, but is a full sized cheesecake and takes longer to make. These mini versions bake up and cool in a fraction of the time and are so delicious with the addition of apples. Plus, you don’t have to worry about water baths, springform pans, or messy slicing.

Closeup of a mini caramel apple cheesecake with a bite taken out of it.

Why You’ll Love These Caramel Apple Mini Cheesecakes

Seeking the perfect fall dessert recipe? This one might just be it. Here’s why.

  • Perfectly sharable. These little cheesecakes are the perfect 2-3 bite dessert to bring to your next fall gathering. Each portion is conveniently packaged in its own wrapper, eliminating the need for messy slicing and serving.
  • Quicker and easier than full-sized. Everyone loves cheesecake but not everyone loves that it takes several hours to make a full-sized version. These mini cheesecakes take a fraction of the time and save you the hassle of a water bath. You can bake them right in the cupcake pan with cupcake liners!
  • Wonderful texture. The creamy, rich texture of these cheesecakes next to the buttery crunch of the graham cracker crusts and the tender, syrupy apples is unbeatable.
  • Fall flavor. Nothing (aside from pumpkin, maybe) screams fall like apples. These mini desserts are exploding with caramel apple flavor, evoking cozy autumn feeling with every bite.
Ingredients for mini caramel apple cheesecakes.

What You’ll Need

Here’s what you’ll need to make these fall-friendly mini caramel apple cheesecakes. Don’t forget to scroll to the recipe card below for exact measurements.

Caramel Layer

  • Caramel sauce – I highly recommend a homemade sauce and use my caramel sauce in these. My salted caramel sauce would also do the trick. Store-bought sauces are often on the thinner side and may not work as well.
  • All-purpose flour – A 1:1 gluten-free flour should work here as well.


  • Graham cracker crumbs – Feel free to use Nilla wafers or even vanilla Oreos here instead.
  • Sugar – For a touch of sweetness in the crust.
  • Ground cinnamon – I love the extra pop of flavor this adds to the crust.
  • Unsalted butter – The butter should be melted.


  • Cream cheese – The cream cheese needs to be at room temperature. If it is too cold, you will end up with a lumpy filling. Also be sure to use brick-style full-fat cream cheese. Tub-style or reduced fat cream cheese can often be too soft.
  • Light brown sugar – You could use regular granulated sugar or brown sugar. I personally love the extra flavor of the brown sugar.
  • All-purpose flour – The flour prevents the egg proteins from over-coagulating, giving you a creamier texture and helping you prevent cracks.
  • Sour cream – This contributes to the creamy texture. You could also use heavy cream.
  • Vanilla extract
  • Eggs – Be sure that your eggs are large in size and at room temperature. Cold eggs will not mix smoothly into the filling.


  • Apples – I like Granny Smith apples here but feel free to pick your favorite. Generally, a tart, firm apple will do best. Honeycrisp would be a great call as well.
  • Fresh lemon juice – To help prevent them from browning too much and add a pop of flavor.
  • Light brown sugar – For a touch of sweetness and flavor.
  • Spices – Ground cinnamon and nutmeg accentuate the flavor of apples beautifully.
  • Caramel sauce – For a drizzle on top.
Overhead of mini caramel apple cheesecakes on a serving platter.

How to Make Mini Caramel Apple Cheesecakes

Ready to make the best mini cheesecakes you’ve ever tasted? Here’s a quick look at how to do it. Be sure to scroll to the recipe card below for more thorough instructions.

Caramel Sauce

  • Make the caramel sauce. Make a batch of my popular caramel sauce.
  • Cool. Mix ½ a cup of the sauce with the flour and set aside to cool. Pour the rest into a separate bowl and chill in the fridge.


  • Prep. Preheat oven to 325°F, line a cupcake pan with cupcake liners, and grease the liners with non-stick spray.
  • Make the crust mixture. Whisk together the graham cracker crumbs, sugar, cinnamon, and melted butter.
  • Bake. Press 2 tablespoons of the mixture into the bottom of each cupcake liner and bake for 5 minutes.


  • Prep. Reduce oven to 300°F.
  • Make the filling. Mix together the cream cheese, brown sugar, and flour. Mix in the sour cream and vanilla extract.
  • Add the eggs. Mix in the eggs, one at a time.
  • Assemble. Spoon 1 tablespoon of the flour-caramel sauce mixture into each cupcake tin and then divide the cream cheese mixture evenly between the tins.
  • Bake. Bake for 20 minutes.
  • Cool gradually. Turn off the oven and leave the door closed for 10 minutes. Crack the oven door and allow the cheesecakes to cool for 15-20 minutes. Transfer the cheesecakes to the fridge to finish cooling before remove them from the pan.


  • Make the apple topping. Cook the apples, lemon juice, brown sugar, cinnamon, and nutmeg over medium heat until the apples are tender.
  • Assemble. Spoon the apples onto the cheesecakes and drizzle with the remaining caramel sauce.
  • Serve. Serve while the apples are still warm.
Mini caramel apple cheesecakes on a serving platter.

Tips for Making Mini Cheesecakes

Do your homework before diving into this delicious recipe. These simple tips and tricks really will make all the difference.

  • Room temperature cream cheese. Start with room-temperature cream cheese. If it is too cold, you will end up with a lumpy filling.
  • Mix slowly and not too much. When making the cheesecake filling, mix on low speed and just until everything is incorporated. Mixing at too high of a speed and/or for too long will incorporate excess air, which can cause the cheesecakes to crack.
  • Scrape the bowl. As you add ingredients to the cheesecake filling and mix them in, scrape down the sides of the bowl intermittently in order to ensure all of the ingredients make it into the mixture.
  • Don’t open the oven. As the cheesecakes bake and then cool in the oven, resist the temptation to check in on them. Opening the oven prematurely will disrupt the baking process and cause them to be under baked.
  • Cool gradually. Once you turn the oven off, allow the cheesecakes to cool inside for 10 minutes before opening the oven just a tad and allowing them to sit for an additional 15 minutes. Then you can transfer them to the fridge. The cheesecakes will continue to cook and firm up during this process and the gradual cooling will help keep them from cracking.
  • Reheat the sauce. If the caramel sauce has become too firm in the fridge to drizzle, reheat it in the microwave in 10-second intervals until it’s warm enough to drizzle.

Proper Storage

  • Refrigerator. Arrange the mini cheesecake in a single layer in an airtight container and store them in the fridge for up to 5 days.
  • Freezer. Spread the cheesecakes out on a cookie sheet and pop them in the freezer for a couple of hours. Once they are firm, transfer them to an airtight container and store them in the freezer for up to 3 months. Allow the cheesecakes to thaw in the fridge before diving in. I recommend freezing them without the apples on top and adding them fresh after thawing.

These little desserts are best enjoyed cool but not too cold. So allow them to sit at room temperature for 15 minutes or so before enjoying.

More Fall Cheesecake Recipes To Try

I’m a big cheesecake fan. I’ve been publishing cheesecake recipes for years now and I’ll tell you, there is one (or many) for every season in my cheesecake recipe collection. Here are some of my favorites for fall.

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Mini caramel apple cheesecakes on a serving platter.

Mini Caramel Apple Cheesecakes

  • Author: Lindsay Conchar
  • Prep Time: 1 hour
  • Cook Time: 45 minutes
  • Total Time: 1 hour 45 minutes
  • Yield: 12 mini cheesecakes
  • Category: Desserts
  • Method: Baking
  • Cuisine: American


Bring these mini caramel apple cheesecakes to your next fall gathering. A creamy cream cheese filling is baked over graham cracker crusts and caramel sauce, then topped with tender spiced apples for the perfect single-serve desserts.


Caramel Layer


  • 1 cup (134g) graham cracker crumbs
  • 2 tbsp (26g) sugar
  • 1/4 tsp ground cinnamon
  • ¼ cup (56g) unsalted butter, melted


  • 12 ounces (339g) cream cheese, room temperature
  • 1/2 cup (112g) packed light brown sugar
  • 2 tbsp (16g) all-purpose flour
  • ½ cup (115g) sour cream
  • 1 1/2 tsp vanilla extract
  • 2 large eggs, room temperature


  • 2 cups (213g) diced Granny Smith apples
  • 1 tsp fresh lemon juice
  • 2 tbsp (28g) light brown sugar
  • ½ tsp ground cinnamon
  • ¼ tsp ground nutmeg
  • Additional caramel sauce, for drizzling, from above


Caramel Sauce

  1. Make the caramel sauce according to the recipe.
  2. Pour ½ a cup of the sauce into a bowl or jar and add the flour. Stir until well combined. Set aside to cool at room temperature.
  3. Pour the rest of the sauce into another bowl or jar. Set in the fridge to cool.


  1. Preheat oven to 325°F (162°C). Add cupcake liners to a cupcake pan. Spray liners with non-stick spray, if desired.
  2. Add the crust ingredients to a small bowl and stir until well combined. Divide the mixture between the cupcake liners (about 2 tablespoons per cup) and press into the bottoms.
  3. Bake the crusts for 5 minutes then remove from oven. Allow to cool while you make the filling.


  1. To make the filling, reduce oven to 300°F (148°C). In a large bowl, mix the cream cheese, brown sugar, and flour until combined (Use low speed to keep less air from getting into the batter, which can cause cracks). Scrape down the sides of the bowl.
  2. Add the sour cream and vanilla extract. Beat on low speed until well combined.
  3. Add the eggs one at a time, beating slowly and scraping the sides of the bowl after each addition.
  4. Divide the caramel sauce with the flour it in between the cupcake liners, about 1 tablespoon per cup.
  5. Divide the filling between the cups until the cups are mostly full.
  6. Bake the cheesecakes for 20 minutes, then turn off the oven and leave the door closed for another 10 minutes.
  7. Crack the oven door and allow cheesecakes to cool for 15-20 minutes, then put in the fridge to finish cooling.
  8. When cheesecakes are cool and firm, remove them from the pan and make the apples. You can leave the cupcake liners on or remove them.


  1. Add the apples, lemon juice, brown sugar, cinnamon and nutmeg to a medium sized pan and cook over medium heat until the apples are tender.
  2. Spoon the apples onto the cheesecakes, then drizzle with remaining caramel sauce. The sauce may be firm from storing in the fridge. Just gently reheat, about 10-15 seconds at a time, it until at your desired temperature.
  3. I recommend serving while the apples are warm. If you want to prep ahead, cook the apples and store them separately in the fridge. Reheat them in the microwave for 15-30 seconds, then spoon them onto the cheesecakes before serving. Cheesecakes are best stored in an airtight container and eaten within 4-5 days.


  • Serving Size: 1 mini cheesecake
  • Calories: 353
  • Sugar: 37.9 g
  • Sodium: 298.2 mg
  • Fat: 16.5 g
  • Carbohydrates: 48.7 g
  • Protein: 5 g
  • Cholesterol: 73.2 mg

Keywords: mini caramel apple cheesecakes, caramel apple mini cheesecakes


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About Lindsay

I'm a wife and a mom to twin boys and a baby girl! And I've got a serious sweets addiction! Bring on the treats!

Scripture I’m Loving

“Come to me, all you who are weary and burdened, and I will give you rest. Take my yoke upon you and learn from me, for I am gentle and humble in heart, and you will find rest for your souls.” Matthew 11:28-29