gluten-free Apple Cheesecake (healthier, refined sugar-free)

This healthier, baked Gluten-Free Apple Cheesecake is everything you need in an easy holiday dessert. It starts with a crunchy, cinnamon crust, creamy cinnamon apple cheesecake filling, and is topped with crumble. It comes together with more wholesome ingredients and is super customizable to fit your dietary needs! Because this apple cheesecake needs a few hours to set, it’s great as a make-ahead dessert!

The best healthy holiday dessert

The other day I was at a girlfriends house and she was making a homemade cheesecake for Friendsgiving. I can’t remember the last time I had a true, baked cheesecake and the wheels in my head started turning. I was dairy-free for YEARS and unfortunately had to miss out on most holiday desserts. However, I recently started incorporating lactose-free, organic products in my diet and wanted to give a lactose-free cheesecake a go! However, this can be made with regular dairy or even dairy-free cream cheese. With all that to say, after three long attempts, I have to say.. it’s perfect.

This cheesecake features an ultra creamy filling full of sautéed cinnamon apples and is topped with a crumble topping (what’s not to love!). This cheesecake is gluten-free and sweetened with coconut sugar and maple syrup, while being creamy, comforting, and surprisingly simple to make — the perfect healthier dessert for holidays, gatherings, or anytime you want something special!

Why You’ll Love This Healthier Apple Cheesecake

• Dietary friendly: This cheesecake is gluten-free, refined sugar-free, and can be made lactose-free or dairy-free.
• Warm cinnamon apples and crumble topping makes it taste like cheesecake meets apple cobbler
• Lower in sugar yet still rich, creamy, and indulgent
• Easy to prepare with simple, more nourishing ingredients

This is the kind of dessert that tastes decadent but won’t leave you feeling weighed down!

Recipe video

Ingredients You’ll Need

The full measurements and recipe are in the recipe card at the bottom of the post!

For the crust:

• Simple Mills Cinnamon Sweet Thins – Simple Mills pecan cookies or Siete cinnamon cookies also work great!
• Coconut oil: You can use grass-fed butter or vegan butter.
• Apples: I prefer sweeter apples, but use your favorite variety! I used SweetTango.
• Creem cheese: Feel free to use regular cream cheese, lactose-free cream cheese, or vegan/dairy-free cream cheese. If using dairy-free cream cheese, be sure to use a THICK brand. I recommend KiteHill. For lactose-free cream cheese, I used Organic Valley.
• Greek yogurt or thick, greek-style coconut yogurt:
• Coconut sugar: Any granulated sweetener should work!
• Eggs: Unfortunately, I haven’t tested this recipe without eggs.
• Vanilla extract, cinnamon, sea salt

For the crumble:

• Almond flour: Light & airy, this creates a slightly crunchy crumble texture! You can sub Tiger Nut flour as a 1:1 substitute.
• Tapioca flour: This helps create the perfect crumble texture.
• Maple syrup
• Pecans: You can also use walnuts or cashews.
• Butter/ghee: grass-fed butter, ghee, or vegan butter all work. I prefer butter over coconut oil as coconut oil makes the crumble brown too fast.
• Cinnamon, vanilla extract, baking powder

How to Make Healthier Baked Apple crumble Cheesecake

Step 1: Cook the apples

Add diced apples to a pan with 1 tbsp oil/butter. Cook for 5-7 minutes until they soften. Then add in the maple syrup, cinnamon, and lemon juice. Cook another 5 minutes until the apples have absorbed the liquid. Set aside to cool.

Step 2: Make the crust & crumble

In a food processor, combine the Simple Mills Sweet Thins and oil/butter and process until a crumb mixture forms. Press this into the bottom of your greased 9″ spring form pan. Set aside. In the food processor, combine all of the crumble ingredients and process until a dough forms. Set aside.

Step 3: Make the Cheesecake Filling

In a food proccesor or in the bowl of a stand mixer, add the cream cheese and blend until smooth and fluffy. Add in the eggs, sugar, vanilla, and sea salt. Blend again until combined. Then add in the yogurt. Be careful not to over-mix. Fold in the cooled apples.

Step 4: Assemble the apple cheesecake

Pour the cheesecake mixture over top of the crust. Then dollop the crumble mixture over top of the cheesecake. I tend to flatten bits and lay it over top.

Step 5: Bake

Bake at 350°F for 45 minutes. The top should be golden and there should be just a tiny bit of jiggle in the center. Cool completely (2 hours) then move to the fridge for at least 3 hours or preferably overnight.

Expert Tips for the Perfect Healthy Apple Cheesecake

• Don’t skip cooling + chilling — this sets the cheesecake and enhances creaminess. I prefer to make mine the night before or morning of, so it has adequate time to set up.
• Use room-temperature ingredients for a smooth, lump-free filling.

How to Store Your Baked apple Cheesecake

• Refrigerator: Up to 5 days in an airtight container
• Freezer: Up to 2 months—freeze slices individually for easy treats
• Best served: Cold or slightly chilled

FAQ

Can I use coconut yogurt instead of Greek yogurt?
You can, but the texture will be slightly softer and less tangy.

Do I have to prebake the crust?
Nope! This crust doesn’t need to be baked prior and I don’t recommend it!

More healthy dessert recipes to try

• Caramel pecan cookie skillet
• Gluten-free apple crisp
• Mini pumpkin cheesecake jars
• Gluten-free pumpkin cake roll
• Pumpkin ice cream sandwiches
• Cookie tiramisu cheesecake
• No-bake caramel apple cheesecake

Healthy Apple Crumble Cheesecake (Gluten & Refined sugar-free)

This baked apple crumble cheesecake is everything you need in an easy holiday dessert. It comes together with more wholesome ingredients and is super customizable to fit your dietary needs! It can be made dairy-free, is refined sugar-free, and gluten-free!

Print Recipe Pin Recipe

Prep Time 20 minutes mins

Cook Time 45 minutes mins

Chill time 3 hours hrs

Total Time 4 hours hrs 5 minutes mins

Course Dessert

Servings 12 slices

Ingredients

  

Crust

• 1 package Simple Mills pecan cookies or sweet thins
• 3 tbsp melted coconut oil or butter

Apples

• 2 large or 3 small apples of choice (I used sweet apples)
• 2 tbsp maple syrup
• 1 tsp cinnamon

Cheesecake filling

• 16oz cream cheese, room temp *see notes
• 1/4 cup greek yogurt or greek style THICK coconut yogurt
• 3/4 cup coconut sugar or other granulated sweetener
• 2 eggs, room temp
• 2 tsp vanilla extract
• pinch of sea salt

Crumble topping

• 1/2 cup almond flour
• 1/2 cup old fashioned rolled oats
• 1/2 cup chopped pecans
• 1/4 cup tapioca flour
• 1/4 cup maple syrup
• 1/4 cup melted grass-fed butter, ghee, or vegan butter
• 1 tsp cinnamon
• 1 tsp baking powder
• 1 tsp vanilla extract & pinch of sea salt

5 minute caramel sauce (optional but amazing! Feel free to use store-bought)

• 1/4 cup coconut cream (solid part from the top of a can of full-fat coconut milk)
• 2 tbsp maple syrup
• 2 tbsp coconut sugar
• 3 tbsp coconut oil
• 1 tsp vanilla extract & 1/2 tsp sea salt

Instructions

 

• Preheat oven to 350F. Grase a 9" springform pan with spray oil.
• Add diced apples to a pan with 1 tbsp oil/butter. Cook for 5-7 minutes until they soften. Then add in the maple syrup, cinnamon, and lemon juice. Cook another 5 minutes until the apples have absorbed the liquid. Set aside to cool.
• In a food processor, combine the Simple Mills Sweet Thins and oil/butter and process until a crumb mixture forms. Press this into the bottom of your greased 9″ spring form pan. Set aside. In the food processor, combine all of the crumble ingredients and process until a dough forms. Set aside.
• In a food processor or in the bowl of a stand mixer, add the cream cheese and blend until smooth and fluffy. Add in the eggs, sugar, vanilla, and sea salt. Blend again until combined. Then add in the yogurt. Be careful not to over-mix. Fold in the cooled apples.
• Pour the cheesecake mixture over top of the crust. Then dollop the crumble mixture over top of the cheesecake. I tend to flatten bits and lay it over top.
• Bake at 350°F for 45 minutes. The top should be golden and there should be just a tiny bit of jiggle in the center. Cool completely (2 hours) then move to the fridge for at least 3 hours or preferably overnight before cutting into slices. I like to top mine with my 5 minute caramel sauce and coconut whipped topping! The longer it has to chill, the better, as it'll set up as it chills. If you don't allow it to chill, it'll be softer/mushier.
• I like to top mine with my 5 minute caramel sauce and coconut whipped topping!

Caramel sauce (Feel free to use store-bought!)

• Simply add everything to a small saucepan. Bring to a boil over medium heat, stirring very frequently. Let boil for 7-8 minutes. Then remove from heat. It'll thicken a bit as it cools!

Video

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