Gluten-Free Apple Pecan Cheesecake Recipe

This Gluten-Free Apple Pecan Cheesecake combines creamy cheesecake with soft cinnamon apples and crunchy pecans for the ultimate fall dessert. Sweet, nutty, and gluten-free!

Alright, listen up, cheesecake lovers! If you’re looking for a fall dessert that’s going to steal the show, then buckle up because this Gluten-Free Apple Pecan Cheesecake is about to change your life. 

Imagine the smooth, creamy decadence of cheesecake combined with the warm, spiced goodness of cinnamon apples and the irresistible crunch of pecans. 

It’s basically all your favorite fall flavors in one glorious, gluten-free package. And honestly, who could ask for more?

This isn’t just any cheesecake, though. We’re talking layers of flavor that will make you want to eat the entire thing in one sitting (no judgment here).

The base is a buttery, gluten-free graham cracker crust that’s crispy and delicious. Then, you’ve got the creamy, vanilla-infused cheesecake that’s rich without being too heavy. 

But the real showstopper? The caramelized apple pecan topping. We’re talking brown sugar, cinnamon, and a touch of butter coming together with tart apples and crunchy pecans to create a topping that’s both sweet and nutty. 

It’s like an apple pie got a serious upgrade and decided to crash the cheesecake party.

Best of all, this dessert is gluten-free without compromising on flavor or texture. 

So, whether you’re avoiding gluten or just want a dessert that screams “fall,” this cheesecake is the perfect choice during apple season. 

It’s easy enough to whip up for a cozy night in but impressive enough to serve at your next holiday gathering. Trust me, this cheesecake is about to be the star of your dessert table!

If you love cheesecake recipes you may also want to try my Gluten-Free Strawberry Cheesecake or my Cookie Dough Cheesecake Bars.

WHY YOU’LL LOVE THIS GLUTEN-FREE APPLE PECAN CHEESECAKE

• Gluten-Free & Fabulous: No gluten? No problem! This cheesecake is totally gluten-free, but no one will be able to tell. It’s all about flavor and texture here—creamy, crunchy, and perfectly sweet.
• Fall in Every Bite: Apples, pecans, cinnamon—this cheesecake is fall in dessert form. It’s the ultimate cozy treat for those chilly evenings when all you want is something sweet with a side of cozy.
• Easy & Impressive: Even if you’re not a seasoned baker, this cheesecake is surprisingly simple to pull off. The apple pecan topping makes it look (and taste) like you spent hours in the kitchen, when really, it’s just a few easy steps.
• Perfect for Any Occasion: Whether you’re hosting Thanksgiving, a Friendsgiving, or just treating yourself (because why not?), this cheesecake is the perfect showstopper. Plus, who doesn’t love the combo of cheesecake and apples? It’s basically a crowd-pleaser.

SIMPLE INGREDIENTS YOU NEED FOR THE GLUTEN FREE CHEESECAKE RECIPE

You will need the following handful of ingredients listed below to make this classic cheesecake (the exact measurements, nutritional information and full recipe are in the printable recipe card at the bottom of the post):

• gluten-free graham cracker crumbs – can pulse graham crackers in high-powered blender
• unsalted butter
• white granulated sugar
• sea salt
• full-fat cream cheese – can use vegan cream cheese if needed
• large eggs
• plain greek yogurt – can also use sour cream if desired
• pure vanilla extract
• brown sugar
• chopped apple slices – use fresh apples and can use granny smith apples, honeycrisp apples, etc.
• pecans
• optional – whipped cream, store-bought graham cracker crust, lemon juice, coconut sugar, white sugar, refined coconut oil, maple sugar, pure maple syrup, etc.

HOW TO MAKE

Making The Gluten-Free Crust

Preheat your oven to 350 degrees F. In a bowl, mix together the graham cracker crumbs, melted butter, sugar, and salt. Press the cheesecake crust mixture into the bottom of a 9-inch springform pan using your hands or a glass and bake for 9-12 minutes.

Making The Cheesecake Filling

In a large bowl with a hand held mixer or in the bowl of a stand mixer with the paddle attachment, beat the cream cheese and sugar together until smooth. Add the eggs, one at a time, fully incorporating each before adding the next. Stir in the Greek yogurt, vanilla extract, and salt.

Pour the filling over the crust in the springform pan. Smooth the top with a spatula and tap the pan on the counter numerous times to release any air bubbles.

Reduce the oven temperature to 325 degrees F. Put the springform pan into a larger roasting pan or baking dish and add hot water to create a water bath. Approximately 1-2 inches of water. 

Bake for 75 minutes, or until the center is just set and the edges are lightly golden. Turn off the oven, open the door slightly and keep it cracked open with a wooden spoon. Let the cheesecake cool inside for 1 hour to prevent cracks.

Remove the cheesecake from the water bath and allow it to reach room temperature. Cover and let chill in the fridge for minimum 4 hours to overnight.

Making The Apple Pecan Topping

Once creamy cheesecake filling has set, make the pecan apple topping. Toss together chopped apples, pecans, brown sugar, and a sprinkle of cinnamon in a skillet with a tiny bit of butter. Sauté until the apples are soft and caramelized, and your kitchen smells like the best fall candle you’ve ever lit.

Pile that gooey, cinnamon-spiced apple pecan topping right on top of your creamy cheesecake layer.

When you’re ready to serve, run a knife around the edge of the pan, then release and remove the springform. Slice, serve, and watch as everyone falls in love with this gluten-free delight!

TIPS AND TRICKS FOR BEST RESULTS

• Room Temp Cream Cheese: Make sure your cream cheese is at room temperature before mixing. It’ll make the filling super smooth and avoid any lumps.
• Don’t Skip the Chill: Cheesecake needs to chill in the fridge for at least a few hours to set properly. If you can, make it the day before your event for maximum flavor and texture.
• Customize the Topping: If you’re feeling adventurous, throw in some dried cranberries or swap out the pecans for walnuts. The topping is super flexible and will still deliver that fall flavor explosion.

STORING LEFTOVER GLUTEN FREE APPLE CAKE

To store leftover Gluten-Free Apple Pecan Cheesecake, cover it tightly with plastic wrap or store it in an airtight container in the refrigerator for up to 4-5 days. 

For longer storage, you can freeze individual slices by wrapping them in plastic wrap and placing them in a freezer bag for up to 3 months. When you’re ready to enjoy, just let the cheesecake thaw in the fridge overnight for that same creamy, delicious texture!

FAQS

CAN I ADD CARAMEL SAUCE TO THIS CHEESECAKE?

Yes! Drizzling some caramel sauce over the top of the cheesecake before serving is a great way to add extra sweetness. It pairs perfectly with the apple pecan topping and gives a more decadent flavor, like a mini pecan pie on top of your cheesecake!

HOW DO I PREVENT CRACKS IN THIS PECAN CHEESECAKE BATTER?

Bake the cheesecake slowly, and avoid opening the oven door during baking. After baking, let it cool slowly in the oven with the door slightly ajar. This helps the cheesecake set without cracking.

HOW DO I KNOW WHEN THE APPLE PECAN CHEESECAKE IS DONE BAKING?

The cheesecake is done when the center is slightly jiggly, but the edges are set. Turn off the oven and leave the cheesecake inside with the door slightly open for an hour to cool gradually. Then transfer it to a wire rack to cool completely.

CAN I MAKE THE APPLE FILLING AHEAD OF TIME?

Yes! You can combine apples with cinnamon, butter, and sugar and cook them in a small saucepan on medium heat until soft. Store in the fridge until you’re ready to use them as your apple filling for the cheesecake.

Other Healthy Desserts For Fall You May Enjoy Trying!

• Pumpkin Pie Protein Ice Cream
• Gluten Free Pumpkin Muffins
• Pumpkin Pie Protein Cheesecakes
• Gluten-Free Pumpkin Chocolate Chip Cookies
• Easy Pumpkin Cake Pops
• Single Serving Apple Crumble
• Pumpkin Spice Energy Balls
• Starbucks Pumpkin Cream Cheese Muffins
• Air Fryer Apple Crisp
• Chocolate Covered Apple Slices
• Baked Apple Cinnamon Oatmeal Cups
• Apple Pie Protein Ice Cream

Continue to Content

Yield: 12 servings

Gluten-Free Apple Pecan Cheesecake Recipe

Print

This Gluten-Free Apple Pecan Cheesecake combines creamy cheesecake with soft cinnamon apples and crunchy pecans for the ultimate fall dessert. Sweet, nutty, and gluten-free!

Prep Time 20 minutes

Cook Time 1 hour 15 minutes

Chill Time 4 hours

Total Time 5 hours 35 minutes

Ingredients

GLUTEN-FREE CRUST

• 1 cup gluten-free graham cracker crumbs
• 1/4 cup butter
• 1 1/2 tbsp white sugar
• pinch of salt

CHEESECAKE FILLING

• 2 8oz package cream cheese
• 2/3 cup white sugar
• 2 eggs
• 2/3 cup plain greek yogurt
• 2 tsp vanilla extract
• 1/2 tsp salt

APPLE PECAN TOPPING

• 1/4 cup butter
• 1/4 cup brown sugar
• 3 honey crisp apples
• 1 tsp cinnamon
• Dash of ground nutmeg
• 1/2 cup pecans

Instructions

1. Making The Gluten-Free Crust: Preheat your oven to 350 degrees F. In a bowl, mix together the graham cracker crumbs, melted butter, sugar, and salt. Press the cheesecake crust mixture into the bottom of a 9-inch springform pan using your hands or a glass and bake for 9-12 minutes.
2. Making The Cheesecake Filling - In a large bowl with a hand held mixer or in the bowl of a stand mixer with the paddle attachment, beat the cream cheese and sugar together until smooth. Add the eggs, one at a time, fully incorporating each before adding the next. Stir in the Greek yogurt, vanilla extract, and salt.
3. Pour the filling over the crust in the springform pan. Smooth the top with a spatula and tap the pan on the counter numerous times to release any air bubbles.
4. Reduce the oven temperature to 325 degrees F. Place a baking dish into the oven underneath the cheesecake and add hot water to create a water bath. Approximately 1-2 inches of water. 
5. Bake for 75 minutes, or until the center is just set and the edges are lightly golden. Turn off the oven, open the door slightly and keep it cracked open with a wooden spoon. Let the cheesecake cool inside for 1 hour to prevent cracks.
6. Remove the cheesecake from the water bath and allow it to reach room temperature. Cover and let chill in the fridge for minimum 4 hours to overnight.
7. Making The Apple Pecan Topping - Once creamy cheesecake filling has set, make the pecan apple topping. In a medium pan over medium heat, melt the butter and brown sugar together until combined and bubbling slightly. Add the apples, cinnamon, and nutmeg, then cook for 7-9 minutes, stirring occasionally, until the apples are tender.
8. Stir in the pecans until they’re well coated and evenly mixed. Pile the cinnamon-spiced apple pecan topping right on top of your creamy cheesecake layer.
9. When you’re ready to serve, run a knife around the edge of the pan, then release and remove the springform. Slice, serve, and watch as everyone falls in love with this gluten-free delight!

Nutrition Information:

Yield:

12

Serving Size:

1
Amount Per Serving: Calories: 370Total Fat: 25gSaturated Fat: 13gTrans Fat: 0gUnsaturated Fat: 10gCholesterol: 90mgSodium: 338mgCarbohydrates: 32gFiber: 2gSugar: 25gProtein: 6g

The nutrition information provided is calculated based on industry-standard software and should be used as a general guide only. The information may vary depending on ingredient substitutions, cooking techniques, and individual serving sizes. It is the responsibility of the reader to ensure the accuracy and appropriateness of the nutritional information provided. Always consult a qualified healthcare provider for personalized medical or nutritional advice.

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