These Salted Caramel Apple Pie Cheesecake Cups bring together three of the best fall flavors: creamy cheesecake, warm cinnamon apples, and rich salted caramel.
They look fancy, but each part is simple to make.
The buttery graham cracker crust gives every cup a little crunch, while the apple pie topping keeps them cozy and homemade.
Makes: 12 cheesecake cups
Prep time: 25 minutes
Bake time: 24 minutes
Cooling and chilling: About 4 1/2 hours
Total time: About 5 hours 20 minutes
Why I Love This Recipe
Apple pie and cheesecake are two desserts I have a hard time choosing between, so these little cups solve that problem nicely. You get the buttery crust and creamy center of cheesecake, but the cinnamon apples on top make every bite taste like apple pie.
I also love making these when I want dessert to feel special without cutting and serving a full cheesecake. The individual portions are easy to put on a dessert table, and most of the work can be finished the day before.
- Three desserts in one: They have cheesecake, apple pie filling, and salted caramel.
- Great texture: You get a crisp crust, smooth filling, soft apples, and silky caramel.
- Easy portions: No slicing a large cheesecake at serving time.
- Make-ahead friendly: Cheesecake actually benefits from several hours in the refrigerator.
- Perfect for fall: Apples, cinnamon, caramel, and vanilla give these cups that classic cozy flavor.
What You’ll Need
For the graham cracker crust
- 1 cup finely crushed graham cracker crumbs
- 3 tablespoons unsalted butter, melted
- 1 tablespoon light brown sugar
- 1/4 teaspoon ground cinnamon
For the cheesecake filling
- 8 ounces full-fat cream cheese, softened to room temperature
- 1/3 cup plain Greek yogurt, room temperature
- 1/4 cup granulated sugar
- 1 large egg, room temperature
- 1 teaspoon vanilla extract
- 1/8 teaspoon fine sea salt
For the apple pie topping
- 1 1/2 cups peeled and diced apple, cut into small 1/4-inch pieces
- 1 tablespoon unsalted butter
- 2 tablespoons light brown sugar
- 1 teaspoon lemon juice
- 1/2 teaspoon ground cinnamon
- 2 tablespoons water
- 1 teaspoon cornstarch
- 1 tablespoon cold water
For the salted caramel topping
- 1/3 cup thick salted caramel sauce
- 1/8 teaspoon flaky sea salt
Recipe and Instructions
Step 1: Prepare the Pan and Heat the Oven
Heat the oven to 350°F (175°C). Place 12 paper liners in a standard 12-cup muffin pan.
Step 2: Make and Bake the Crust
In a medium bowl, stir together 1 cup finely crushed graham cracker crumbs, 3 tablespoons melted unsalted butter, 1 tablespoon light brown sugar, and 1/4 teaspoon ground cinnamon. The mixture should look like damp sand.
Divide the mixture evenly among the 12 liners, about 1 1/2 tablespoons per cup. Press it firmly into an even layer. Bake at 350°F (175°C) for 6 minutes. Leave the oven on.
Step 3: Mix the Cheesecake Filling
Beat 8 ounces softened full-fat cream cheese with 1/4 cup granulated sugar on low to medium speed until smooth. Add 1/3 cup room-temperature plain Greek yogurt, 1 teaspoon vanilla extract, and 1/8 teaspoon fine sea salt. Mix just until creamy.
Add 1 room-temperature large egg and mix on low only until the egg disappears into the filling. Do not keep beating once it is smooth.
Step 4: Fill and Bake the Cheesecakes
Divide all of the cheesecake filling evenly among the 12 warm crusts. Each cup should be roughly three-quarters full.
Bake at 350°F (175°C) for 17 to 19 minutes. The edges should look set, while the very centers should still have a slight wobble.
Remove the pan from the oven. Cool the cheesecakes in the pan for 30 minutes, then refrigerate for at least 4 hours, or overnight.
Step 5: Cook the Apple Pie Topping
Place 1 1/2 cups peeled apples diced into 1/4-inch pieces, 1 tablespoon unsalted butter, 2 tablespoons light brown sugar, 1 teaspoon lemon juice, 1/2 teaspoon ground cinnamon, and 2 tablespoons water in a small saucepan.
Cook over medium heat for about 5 to 7 minutes, stirring often, until the diced apples are tender but still hold their shape.
In a small bowl, whisk 1 teaspoon cornstarch with 1 tablespoon cold water. Pour the slurry into the apples. Cook for another 30 to 60 seconds, stirring, until the sauce turns glossy and thick enough to coat the diced apples.
Remove from the heat and cool completely.
Step 6: Add the Apple Topping
Once both parts are completely cool, remove the cheesecakes from the muffin pan. Spoon the cooled apple pie mixture evenly over all 12 cheesecakes, using about 2 tablespoons of apple topping per cheesecake.
Step 7: Finish With Salted Caramel
Drizzle 1/3 cup thick salted caramel sauce evenly over the 12 apple-topped cheesecakes. Finish with 1/8 teaspoon flaky sea salt, using just a small pinch over each cup.
Serve cold or let the cheesecakes sit at room temperature for about 10 minutes for a softer, creamier texture.
Why This Recipe Works (Quick Science)
The cream cheese gives the filling its rich structure, while Greek yogurt adds moisture and a slight tang. Using room-temperature ingredients helps them blend smoothly without needing lots of mixing.
The egg sets the cheesecake as it heats. Mixing it in gently is important because too much trapped air can puff the cheesecakes in the oven and make them sink or crack as they cool.
For the apples, heat softens their structure while sugar draws out their juices. The cornstarch slurry then thickens those juices into a glossy apple pie sauce. Cooling the apples before adding them to the cheesecakes keeps the creamy filling firm.
The prebaked graham cracker crust also matters. Those first 6 minutes help set the butter and sugar so the crust is less likely to become soggy under the cheesecake.
Pro Tips
- Use room-temperature cream cheese, yogurt, and egg. Cold ingredients are harder to blend and can leave lumps.
- Cut the apples into small, even 1/4-inch pieces. Large chunks are harder to keep on these little cheesecakes.
- Once the egg goes in, mix gently and briefly. That helps keep the tops smooth.
- Don’t wait for the centers to become completely firm in the oven. A slight wobble means the cheesecake will stay creamy after chilling.
- Let the apple topping cool before assembly. Warm apples can soften the chilled cheesecake.
Tools You’ll Need
- Standard 12-cup muffin pan
- 12 paper muffin liners
- Medium mixing bowl
- Small mixing bowl
- Electric hand mixer
- Silicone spatula
- Measuring cups
- Measuring spoons
- Small saucepan
- Wooden spoon
- Small whisk
- Spoon
- Cooling rack
- Round serving plate
Common Mistakes
Overmixing the egg: This adds too much air and can cause the cheesecakes to rise quickly, crack, and then sink.
Overbaking: The centers should still wobble slightly when the pan comes out. A completely firm center can mean a dry cheesecake after chilling.
Using cold cream cheese: Cold cream cheese tends to leave little lumps. Give it enough time to soften first.
Cutting the apples too large: Small diced apples sit neatly on the cups and give you apple in every bite.
Adding hot apples to cold cheesecake: Cool the topping first or it can soften the cheesecake.
Skipping the chilling time: Four hours may feel long, but this is when the filling becomes properly firm and creamy.
Substitutions and Variations
For a gluten-free version, use gluten-free graham crackers. You can replace Greek yogurt with full-fat sour cream in the same amount.
Granny Smith apples give you a tart apple pie flavor, while Honeycrisp or Pink Lady apples make the topping a little sweeter. A mixture of tart and sweet apples works well too.
For more crunch, sprinkle finely chopped toasted pecans over the caramel just before serving. You can also add a tiny pinch of nutmeg to the apples for a warmer spice flavor.
Store-bought thick salted caramel works well, or use your favorite homemade caramel sauce.
Make-Ahead Tips
These are especially good for making ahead. Bake and chill the cheesecakes up to 2 days before serving. The apple topping can also be cooked up to 2 days ahead and refrigerated separately.
For the neatest presentation, add the apples and caramel a few hours before serving rather than several days ahead.
What to Serve With
These cheesecake cups are rich, so simple drinks and sides work best. Try them with hot coffee, cold milk, chai tea, or hot apple cider.
For a fall dessert spread, they also pair nicely with fresh apple slices, toasted pecans, vanilla ice cream, or lightly sweetened whipped cream.
Macros Information
Estimated nutrition per cheesecake cup, based on 12 servings:
- Calories: about 260
- Protein: about 4 g
- Carbohydrates: about 31 g
- Fat: about 14 g
- Fiber: about 1 g
- Sugar: about 22 g
These are estimates. The exact macros will change depending on the graham crackers, Greek yogurt, cream cheese, apples, and salted caramel sauce you use.
Leftovers and Storage
Keep leftover cheesecake cups in an airtight container in the refrigerator for up to 4 days.
For the best texture, don’t leave them at room temperature for more than about 2 hours.
You can also freeze the plain cheesecakes before adding the apple topping and caramel. Wrap them well and freeze for up to 1 month. Thaw overnight in the refrigerator, then add the apples and caramel before serving.
FAQ
What apples are best for these cheesecake cups?
Granny Smith is a great choice because its tart flavor balances the sweet caramel. Honeycrisp, Pink Lady, or a combination of apples also works well.
How do I know when the cheesecakes are done?
The outside edges should look set, but the centers should still have a small wobble when you gently move the pan.
Can I use sour cream instead of Greek yogurt?
Yes. Replace the 1/3 cup Greek yogurt with 1/3 cup full-fat sour cream.
Can I make these without paper liners?
Silicone muffin liners work well too. If using a bare metal muffin pan, removal is much harder, so liners are recommended.
Why did my cheesecake cups sink?
A little dip in the middle is normal and actually gives the apple topping a nice place to sit. A deep collapse can happen if the filling was overmixed or the cheesecakes were underbaked.
Can I use canned apple pie filling?
Yes. Chop the apple pieces smaller if needed and use about 2 tablespoons per cheesecake. Homemade topping gives you more control over sweetness and texture.
Can I use homemade salted caramel?
Absolutely. Just let it cool until it is thick enough to drizzle without running straight off the cheesecakes.
Final Thoughts
These Salted Caramel Apple Pie Cheesecake Cups have a little bit of everything: buttery graham cracker crust, creamy cheesecake, cinnamon apples, and that final salty-sweet caramel drizzle. They are simple enough for a weekend baking project but pretty enough to bring out for a fall party or holiday dessert table.
Give them plenty of time to chill, pile on those glossy apples, and don’t skip that little pinch of flaky salt at the end. If you make them, leave a comment and share how yours turned out or any questions you had along the way.
