Gluten Free Caramel Apple Cheesecake Bars

These gluten-free caramel apple cheesecake bars have a simple shortbread base paired with a smooth cheesecake layer, fresh spiced apples, and a crumbly topping. Top with a drizzle of salty caramel sauce for extra sweetness. This recipe is perfect for any fall occasion and would be delicious on your Thanksgiving dessert table!
A metal spatula lifting a gluten free apple caramel cheesecake bar with streusel out of a pan of additional gluten free cheesecake bars.
A stack of three gluten free caramel apple cheesecake bars on a dessert plate.

These gluten-free caramel apple cheesecake bars have the perfect blend of rich creaminess and fresh, fruity tang. Each bite gives a gentle contrast of velvety cheesecake and the slight crunch of apple pieces. 

We start with a buttery gluten-free shortbread crust that is topped with a layer of rich cheesecake. We spoon spiced apples over the cheesecake and sprinkle a gluten-free crumb topping in the crevices. Once baked, a drizzle of salted caramel sauce completes this delicious gluten-free dessert. 

At first glance, these apple caramel cheesecake bars might seem like a dessert with many components, but don’t let that deter you. Each layer, from the crumbly shortbread base to the velvety cheesecake, the tart spiced apples, and the crisp crumble topping, is simple to prepare. While the recipe takes a step-by-step approach, each stage is straightforward, making the entire process manageable even for novice bakers. And the end result? Absolutely worth every moment spent.

These bars are versatile, making them just as suitable for a weekend family gathering as they are for a casual Tuesday evening dessert. Best of all? You can make them ahead of time which makes them my go-to for Thanksgiving. If you’re after a reliable dessert that’s both familiar and a little special, these bars are always one of my top picks that the whole family will enjoy.

You’ll love this recipe because:

  • It’s easy to make ahead. Prepare these bars in advance and store them in the refrigerator. They’ll remain fresh and delicious for up to 4 days, ensuring you have a delightful treat ready whenever you need it.
  • There’s texture in every bite. From the firm base to the soft cheesecake, and the slightly crunchy apples topped with a crumbly finish, each layer offers a distinct texture, making every bite interesting.
  • It’s gluten-free. This recipe is made gluten-free by using Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour, so whether you have celiac disease, a gluten intolerance, or a wheat allergy, you can enjoy these gluten-free cheesecake bars! And I promise you, no one will be able to tell they’re gluten-free!

Ingredients

Ingredients in small bowls to make gluten free caramel apple cheesecake bars, including brown sugar, green apples, caramel sauce, granulated sugar, ground cinnamon, melted butter, eggs, gluten-free flour, two sticks of unsalted butter, salt, three cream cheese bricks, vanilla extract and ground nutmeg with text overlays over each ingredient.

Ingredient Notes

  • Gluten-free flour blend – I tested this recipe with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag), which already contains xanthan gum. This is a blend that is meant to be swapped in a 1:1 ratio with all-purpose flour. I cannot verify that other brands of gluten-free flour will work, as I have not tested them. Also remember that different flour blends will weigh different amounts. I’ve found this blend weighs 144g per 1 cup, whereas typical all-purpose flour weighs 120g per 1 cup. For best results, use the metric measurements that I’ve provided in the recipe card below. 
  • Granulated sugar – Regular white sugar works best for the crust, but you can also use brown sugar if you prefer. 
  • Unsalted butter – Ensure your butter is softened, not melted, for the best texture. If you only have salted butter on hand, omit the additional salt from the recipe. For the crumb topping, I use melted butter, but you can also use softened butter instead if you prefer. I just think melted butter is easier for that step. 
  • Cream cheese – Full-fat cream cheese is recommended for the creamiest texture. Make sure it’s softened to room temperature for easy blending. If you need to quickly soften the cream cheese, place the foil wrapped cream cheese bricks in a bowl of warm water for 5-10 minutes until softened.
  • Brown sugar – Light brown sugar is typically used in recipes for its mild molasses flavor, but dark brown sugar can be used for a deeper molasses taste in this recipe if you prefer.
  • Eggs – It’s best to use fresh, large eggs. My large eggs weigh 50g each (measured with the shell on). Ensure the eggs are at room temperature to mix seamlessly into the batter.
  • Vanilla extract – Use pure vanilla extract for the best flavor. Avoid imitation vanilla as it doesn’t provide the same depth of flavor.
  • Ground cinnamon – Just a little bit of cinnamon is added to the cheesecake filling to give it a little warmth. It’s also used in the apple topping which gives them a ton of flavor. 
  • Granny Smith apples – This variety is tart and holds up well during baking without getting mushy. If you prefer a sweeter apple, you can use Honeycrisp or Fuji, but the tartness of Granny Smith balances the sweetness of the bars well.
  • Ground nutmeg – A little goes a long way to spice the apple mixture. 
  • Caramel sauce – To make this recipe easier, I used a store-bought salted caramel sauce from Mrs. Richardson’s brand, which is found at most local grocery stores. While this brand is not certified gluten-free, it has minimal ingredients, none of which contain gluten. 

Always measure your gluten-free flour by weight, not volume. This ensures accuracy and consistency in your baked goods. Different blends can have varying densities, so using a scale guarantees the same amount each time, leading to perfect results.

Step-by-Step instructions

These gluten free apple caramel cheesecake bars may seem like they have a lot of components, but each layer is very easy to make. The below steps with matching photos are not meant to be the full recipe, but instead to help you see the recipe made at various stages so you can make these caramel apple cheesecake bars perfectly every time!

For the ingredient list with measurements, full instructions, printable recipe, and additional notes, please scroll down to the recipe card.

A pastry cutter that is cutting butter into a gluten-free flour mixture in a glass mixing bowl.
Combine the gluten-free flour, sugar and salt in a mixing bowl. Whisk to combine. Add the softened butter and use a pastry cutter or two knives to cut the butter into the flour mixture until crumbly. You should be able to pinch the dough together between two fingers.
A parchment lined metal baking pan that has a pile of gluten-free shaggy dough to make a shortbread crust layer for cheesecake.
Pour the shortbread mixture into a prepared 9×13-inch baking pan.
An overhead view of a rectangular baking pan lined with parchment paper that has a gluten-free shortbread crust pressed into it before baking in the oven.
Use your hands or the back of a measuring cup to press the shortbread into a single, even layer.
A gold metal rectangular baking pan lined with parchment paper and filled with a golden baked gluten-free shortbread crust.
Bake in the oven for until the shortbread is cooked through and the edges are golden brown. Let cool while you prepare the remaining layers.
A glass mixing bowl with softened cream cheese that has been topped with brown sugar before mixing together.
Add the softened cream cheese and brown sugar to a mixing bowl. Mix for 1-2 minutes, until smooth and combined.
A glass mixing bowl with a cheesecake filling mixture topped with one egg before mixing together.
Add the eggs, one at a time, mixing in between each addition just until combined.
A glass mixing bowl with a cheesecake filling topped with vanilla extract and ground cinnamon.
Add the vanilla extract and ground cinnamon to the cheesecake mixture. Mix until combined.
A metal rectangular baking pan lined with parchment paper and filled with a cheesecake batter before baking in the oven.
Pour the cheesecake mixture over the baked shortbread crust. Use an offset spatula to smooth the cheesecake filling into an even layer.
A glass mixing bowl with diced granny smith apples in it that has been mixed together with ground cinnamon and brown sugar with a blue rubber spatula.
Prepare the apples by peeling, coring and cubing into 1/2 inch pieces. Then combine with brown sugar, cinnamon and nutmeg. Toss until combined.
A rectangular baking pan filled with a cheesecake mixture topped with cinnamon spiced apple chunks before baking in the oven.
Sprinkle the apple mixture evenly over the cheesecake layer.
A glass mixing bowl with a gluten-free streusel topping that has been mixed together with a purple rubber spatula.
Prepare the gluten-free streusel by whisking together the gluten-free flour, brown sugar, and cinnamon in a bowl. Then, top with melted butter. Use a spatula to mix until combined and large clumps form.
A rectangular baking pan filled with a cheesecake filled topping with spiced granny smith apple cubes and gluten-free cinnamon streusel before baking in the oven.
Sprinkle the streusel topping over the apple, filling in the gaps.
An overhead view of a rectangle baking pan filled with gluten-free apple cheesecake bars with streusel after coming out of the oven.
Bake for 30-40 minutes, until the cheesecake is cooked through. The edges will be set and the center still jiggly when lightly shaken.
A metal spatula lifting a gluten free apple caramel cheesecake bar with streusel out of a pan of additional gluten free cheesecake bars.
Let cool completely and refrigerate before slicing and serving with a drizzle of caramel sauce.

Recipe FAQs

  • Can I use a different type of apple? Yes, while Granny Smith apples are recommended for their tartness and firm texture, other apple varieties like Honeycrisp, Fuji, or Pink Lady can be used. Just note that the sweetness level might vary.
  • What can I use if I don’t have a gluten-free flour blend? You can use your favorite gluten-free graham cracker for the base of the cheesecake bars instead. You’ll also need some gluten-free flour in the crumb topping, but ground gluten-free oats or almond flour can be used instead if you prefer. 
  • Do I have to add the crumble topping? The crumble topping adds a delightful texture and contrast to the tart apples and creamy cheesecake. However, if you prefer, you can omit it or replace it with chopped nuts.
Can I use a different type of apple?

Yes, while Granny Smith apples are recommended for their tartness and firm texture, other apple varieties like Honeycrisp, Fuji, or Pink Lady can be used. Just note that the sweetness level might vary.

What can I use if I don’t have a gluten-free flour blend?

You can use your favorite gluten-free graham cracker for the base of the cheesecake bars instead. my gluten-free graham cracker crust is perfect for this recipe. You’ll also need some gluten-free flour in the crumb topping, but ground gluten-free oats or almond flour can be used instead if you prefer. 

Do I have to add the crumble topping?

The crumble topping adds a delightful texture and contrast to the tart apples and creamy cheesecake. However, if you prefer, you can omit it or replace it with chopped nuts.

expert tips

  • Use softened butter. Softened butter is key for the crust. If you forgot to take it out of the refrigerator in advance, microwave it in short 5-second bursts, checking in between until it’s soft but not melted.
  • The key to a creamy cheesecake layer. To achieve a smooth cheesecake layer, ensure your cream cheese is truly at room temperature. Cold cream cheese can lead to a lumpy batter.
  • Avoid overmixing. While it’s essential to have a smooth batter, overmixing can introduce too much air, which might affect the texture of the cheesecake layer. Mix just until combined.
  • Don’t rush the cooling time. Resist the urge to cut into the bars right away. Letting them cool completely ensures they set properly, making them easier to slice and giving the flavors time to meld.
  • DO NOT OVERBAKE! I made this mistake on my first test and the bars were gritty, eggy, and did not at all taste like cheesecake. When it’s ready to come out of the oven, the cheesecake edges should appear slightly puffed and set, but the center will still be a bit wobbly or jiggle slightly when you gently shake the pan. As the bars cool, the residual heat will continue to cook and set the center. The internal temperature of cooked cheesecake should be right about 170F in the center, 180F when tested 1-inch from the edge of the bars. 

Storage instructions

  • Storage: After allowing the Caramel Apple Cheesecake Bars to cool to room temperature, transfer them to an airtight container. They can be stored in the refrigerator for up to 4 days. It’s recommended to place a sheet of parchment or wax paper between layers if you stack them to prevent sticking. For best results, don’t drizzle with caramel sauce until you’re ready to serve. 
  • Freezer Option: Once cooled, individual bars can be wrapped tightly in plastic wrap and then placed inside a zip-top freezer bag. Label and date the bag. Properly stored, the bars can be frozen for up to 3 months. To enjoy, allow them to thaw in the refrigerator overnight before serving.
  • Reheat: While these bars are typically enjoyed cold or at room temperature, if you prefer them slightly warmed, place a bar in the microwave and heat for about 10-15 seconds. Be cautious not to overheat as the cheesecake layer can become too soft. 

A stream of caramel sauce being drizzled over a gf apple caramel cheesecake bar on a dessert plate.

Did you make this recipe?

I’d love to know! Please rate it and leave a comment below. You can also share your pictures and tag @adashofmegnut on Instagram.

A metal spatula lifting a gluten free apple caramel cheesecake bar with streusel out of a pan of additional gluten free cheesecake bars.

Gluten-Free Caramel Apple Cheesecake Bars

These gluten-free caramel apple cheesecake bars have a simple shortbread base paired with a smooth cheesecake layer, fresh spiced apples, and a crumbly topping. Top with a drizzle of salty caramel sauce for extra sweetness. This recipe is perfect for any fall occasion and would be delicious on your Thanksgiving dessert table!
5 from 1 vote
Print Pin Rate
Course: Dessert
Cuisine: American
Diet: Gluten Free
Prep Time: 20 minutes
Cook Time: 1 hour 5 minutes
Cooling Time: 3 hours
Total Time: 4 hours 25 minutes
Servings: 18 servings
Calories: 491kcal
Author: Megan

Ingredients

For the crust:

  • 2 cups gluten-free flour blend (288g)
  • 1/2 cup granulated sugar (100g)
  • 1/2 teaspoon salt
  • 1 cup unsalted butter (room temperature (226g))

For the apple layer:

  • 3 cups Granny Smith apples (peeled, cored, chopped into 1/2 inch pieces (from 3-4 small apples that weigh approximately total of 1 lb or 453g))
  • 2 tablespoons brown sugar (25g)
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon ground nutmeg

For the cheesecake layer:

  • 24 oz full-fat cream cheese (room temperature (678g))
  • 3/4 cup brown sugar (150g)
  • 3 large eggs (150g)
  • 2 teaspoons vanilla extract
  • 1/2 teaspoon ground cinnamon

For the crumble topping:

  • 3/4 cup gluten free flour blend (108g)
  • 3/4 cup brown sugar (150g)
  • 1 1/2 teaspoons ground cinnamon
  • cup unsalted butter (melted (76g))

For serving:

  • 1 cup caramel sauce (homemade or store-bought)

Instructions

For the shortbread crust:

  • Preheat the oven to 350F. Grease a 9×13-inch baking dish or line with parchment paper. Set aside.
  • Add the gluten-free flour blend, granulated sugar, and salt to a medium bowl. Whisk to combine.
  • Add the butter and use a pastry cutter to cut the butter into the flour mixture. It will be crumbly.
  • Evenly press the crust mixture into the bottom of the prepared 9×13-inch baking dish, creating a uniform layer.
  • Bake at 350F for 20-25 minutes, until golden brown. Let cool for at least 10 minutes.

For the apple layer:

  • Peel and dice the apples as directed and place in a small mixing bowl.
  • Add the brown sugar, cinnamon and ground nutmeg. Toss until coated. Set aside while you prepare the cheesecake layer.

For the cheesecake layer:

  • Add the cream cheese to a large bowl. Beat on medium speed for 1-2 minutes, until creamy.
  • Then, add in the brown sugar and mix together for another 1-2 minutes, until smooth.
  • Add the eggs, one at a time, mixing in between each addition. Be sure not to overmix as that will create too much air in the batter.
  • Then, mix in the vanilla and cinnamon just until combined. Set aside.

For the crumble topping:

  • Add the gluten-free flour, brown sugar, and cinnamon to a small bowl. Whisk to combine.
  • Pour in the melted butter and stir until the mixture is wet and forms clumps. Set aside.

To assemble:

  • Pour the cheesecake mixture over the semi-cooled shortbread crust.
  • Then, dollop the apples in a single layer over the cheesecake filling.
  • Top with the gluten-free crumble mixture.
  • Bake at 350F for 30-40 minutes, until the cheesecake is set, being sure not to overbake the cheesecake bars. The cheesecake is ready when it’s set along the edges and has a slight jiggle in the center. If you insert a thermometer into the center of the cheesecake bars, it should read 170F.
  • Let the bars cool to room temperature for 1-2 hours before transferring to the refrigerator until ready to serve.
  • Drizzle with caramel sauce before slicing and serving the cheesecake bars.

Notes

  • If you have celiac disease or are on a gluten-free diet for any reason, always double check that your ingredients are gluten-free as manufacturing practices and recipes can change from time to time. 
  • This recipe was tested with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour, which already contains xanthan gum. I cannot verify that other brands of gluten-free flour will work in this recipe as I have not tested them. 
  • Oven temperatures can vary, so it’s a good idea to start checking your cheesecake a few minutes before the suggested baking time is up. The cheesecake should be set at the edges but still have a slight jiggle in the center.
  • I used granny smith apples in this recipe, but you can use other crisp apples in its place. 
  • Store leftover cheesecake bars in the refrigerator for up to 4 days or freeze them in an airtight container for up to 3 months. Thaw individual bars in the refrigerator overnight, or until softened.

Nutrition

Calories: 491kcal | Carbohydrates: 51g | Protein: 6g | Fat: 31g | Saturated Fat: 19g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 8g | Trans Fat: 1g | Cholesterol: 111mg | Sodium: 245mg | Potassium: 124mg | Fiber: 3g | Sugar: 36g | Vitamin A: 1096IU | Vitamin C: 1mg | Calcium: 85mg | Iron: 1mg
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about megan

I’m Megan

A gluten-free food blogger from Chicago and lover of all things food, showing you gluten-free can be easy and delicious, too. Let’s make gluten-free stress free together! Read more…

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