This healthy gluten-free apple crisp recipe is packed with warm spices, oats, nuts, and crisp Granny Smith apples. The beauty of this fall dessert—you’d never know it was made healthier or gluten-free. It doesn’t skimp on flavor one iota!

apple crisp in a white oval baking dish set on a wood table. three scoops of ice cream set on top of the crisp with and a black spoon set in the crisp.

This recipe is: 

  • Gluten-free 
  • Warm – like spice warm 
  • Crispy
  • Versatile 
  • Easy to make 
  • Make-ahead friendly
  • Just sweet enough  

What you’ll need for this healthy apple crisp recipe:

How to make healthy apple crisp (step-by step images)

step-by-step grid of images showing how to make bake healthy gluten-free apple crisp

Gluten-free apple crisp 

This gluten-free apple crisp is made with no refined flour—instead it features old-fashioned rolled oats and almond flour. Just be sure to seek out certified gluten-free oats if necessary.  

Fruit crisps are easy to make gluten free—nothing needs to rise during baking and gluten formation isn’t necessary. All of this means you can swap out the flour for something a bit more nutritionally dense (and something gluten-free!) without requiring a long list of ingredients. 

white bowl with melted ice cream and apple crisp set on a wooden table with a black spoon set in bowl

Healthy apple crisp

I want to stipulate—just because something is gluten-free doesn’t mean it’s healthy. I developed this to be healthier than classic apple crisp recipes and to be gluten-free (inclusivity ya know).

When developing healthyish desserts, my goal is to create desserts that are equal to their predecessor in character while being made intentionally with wholesome ingredients. And that’s on full display in this apple crisp recipe!

A quick rundown of how this apple crisp is healthier than classic recipes:

  • Decreased the overall fat content.
  • Substituted some of the butter with extra-virgin olive oil.
  • Added no refined flour, and instead opted for whole-grain old-fashioned oats, almond flour, and nuts for a granola-like topping. 
  • Added no brown sugar or white sugar, and instead use natural coconut sugar.  
  • Used Granny Smith apples instead of sweeter varieties. 

This apple crisp recipe is a great example of how we cook around here—healthyish. Here at ZK we make smart ingredient swaps to create healthier, more nutritious, and more wholesome dishes without sacrificing on flavor.

Which is why you still see butter in this recipe! A good apple crisp just needs butter. But it doesn’t need a cup or even half of a cup of butter—a quarter cup does the job wonderfully.

It’s also why I still use sugar. I just use a more wholesale option, and I use less of it. Because I want you to taste all of the components—not just sweetness. 

Love all kinds of crisps? Check out this Healthy Cherry—Almond Crisp (also gluten-free)!

close up of apple crisp with melted ice cream dripping over it


Nowadays it’s pretty easy to find coconut sugar. If you’ve never bought it before, look for it in the baking aisle next to the other sugars.

I prefer coconut sugar over most refined sugars (regular cane and brown sugar) because it’s far less processed. But let me be clear, it’s still sugar and it’s still metabolized like sugar in your body.

However, one of the benefits of coconut sugar is that it has a lower glycemic index than refined sugar. This means it’s metabolized slower in the body and causes a lower and slower rise in blood sugar levels.

Now that you have coconut sugar, you may be curious how else you can use it. You’re in the right place! Use coconut sugar in these Healthy-ish Cinnamon Rolls, Homemade Graham Crackers, Healthier Puppy Chow, and Fruit Tart with Mascarpone Whipped Cream & Whole-Wheat Olive Oil Crust.

white bowl with melted ice cream and apple crisp set on a wooden table with a black spoon set in bowl

Best apples for apple crisp

I prefer to use tart and crisp apples, like Granny Smith, for apple crisps. For one thing, their tart flavor balances nicely with the sweet topping and the coconut sugar they’re cooked in.

And second, their crisp texture holds up well to longer bake times. Because of this, the apples can bake long enough to develop flavor and achieve a crisp topping without becoming overcooked and mushy.

If you prefer a slightly sweeter filling, substitute half of the apples with Honeycrisp or Braeburn. And if you prefer an uber traditional and sweet filling, use Golden Delicious, Jonagold and/or Braeburn.

apple crisp in a white oval baking dish set on a wood table. three scoops of ice cream set on top of the crisp with and a black spoon set in the crisp.

How to store apple crisp

Homemade apple crisp will last up to 4 days in the refrigerator covered tightly with plastic. Reheat individual servings in the microwave for 1 minute on high. Or reheat multiple servings in the baking dish in a 300-degree oven for 5–10 minutes.

Variations on this healthy apple crisp recipe

  • Swap the cinnamon and nutmeg for more bold spices like clove, allspice, or cardamom.
  • Swap the pecans for sliced or slivered almonds, walnuts, and/or pepitas (pumpkin seeds).
  • Use sweeter apples (Honeycrisp, Braeburn, Golden Delicious, and/or Jonagold) for a sweeter filling.
  • Add some shredded unsweetened coconut to the topping mixture for additional flavor and texture.
white bowl with melted ice cream and apple crisp set on a wooden table with a black spoon set in bowl

More apple recipes you may like…

Gluten-free desserts you may like…

close up of apple crisp with melted ice cream dripping over it

Make sure to tag me @ZESTFULKITCHEN ON INSTAGRAM or tag #zestfulkitchen on social media if you make a recipe! 

Don’t forget, if you make this Healthy Apple Crisp, leave a comment and rating below!

Pin this recipe and save it for later by clicking the button on any photo. You can also click the red button on the bar below the recipe. Happy baking!

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apple crisp in a white oval baking dish set on a wood table. three scoops of ice cream set on top of the crisp with and a black spoon set in the crisp.

Healthy Gluten-Free Apple Crisp

  • Author: Lauren Grant
  • Prep Time: 15 minutes
  • Cook Time: 1 hour 5 minutes + 20 minutes cooling time
  • Total Time: 1 hour 40 minutes
  • Yield: 46 servings 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American
  • Diet: Gluten Free


Full of warm spices, a splash of bourbon, and coconut sugar, this homemade healthy apple crisp recipe is full of fall flavor!

Made with tart Granny Smith apples, old-fashioned oats, almond flour, and pecans, this dessert is saucy, crunchy, and crispy. Plus, it’s gluten-free, which makes it perfect for a crowd! 




  • ¼ cup coconut sugar 
  • ¼ cup unsalted butter, melted (or ghee, or coconut oil)
  • 2 tablespoons extra-virgin olive oil 
  • ½ teaspoon ground cinnamon 
  • ¼ teaspoon freshly grated nutmeg* 
  • ⅛ teaspoon kosher salt 
  • ⅓ cup packed almond flour (or almond meal)
  • ¾ cup old-fashioned oats
  • ⅓ cup chopped pecans 


  • 3 pounds Granny Smith apples, peeled and cored (7 apples), cut into ½ inch wedges 
  • 3 tablespoons coconut sugar (or brown sugar)
  • 1 tablespoon bourbon (or water)
  • 1 tablespoon fresh lemon juice 
  • 2 teaspoons arrowroot starch (or cornstarch)
  • ¾ teaspoon ground cinnamon
  • ⅛ teaspoon freshly grated nutmeg* 
  • ⅛ teaspoon kosher salt


Heat oven to 400ºF with rack set in middle position.

For the topping, combine sugar, butter, oil, ½ teaspoon cinnamon, ¼ teaspoon nutmeg, and ⅛ teaspoon salt together in a medium bowl. Add almond flour and stir to combine. Add oats and pecans and mix until a thick dough comes together. Cover and chill until needed. 

For the filling, toss apples with coconut sugar, bourbon, lemon juice, arrowroot starch, ¾ teaspoon cinnamon, ⅛ teaspoon nutmeg, and ⅛ teaspoon salt together in a large bowl. Transfer to an 8×8-inch baking dish (or 2-quart baking dish), cover with foil and set on a baking sheet. Bake until apples are juicy and tender, about 50 minutes, stirring halfway through.

Carefully stir apples to distribute juices, then pinch topping into ½-inch pieces and sprinkle in an even layer over top of apples. Bake, uncovered, until filling is bubbly and topping is deep golden brown, about 15 minutes, rotating half way through baking. Transfer to a wire rack and let cool 20 minutes. 

Serve with vanilla ice cream, if desired.


Freshly grated nutmeg is much stronger in flavor than pre-ground nutmeg. If you already have pre-ground nutmeg, go ahead and use that. But if you’re interested, grab some whole nutmeg and use a microplane to grate the nutmeg. Store whole nutmeg in their original jar in the freezer to retain freshness. You can grate the nutmeg straight from the freezer, no need to thaw.


  • Serving Size: ⅙ recipe
  • Calories: 292
  • Sugar: 34g
  • Sodium: 97mg
  • Fat: 14g
  • Saturated Fat: 6g
  • Carbohydrates: 44g
  • Fiber: 7g
  • Protein: 1g
  • Cholesterol: 20mg

Keywords: healthy apple crisp, gluten-free apple crisp, homemade apple crisp, apple crisp recipe, healthy apple crisp recipe, gluten-free apple crisp recipe

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About The Author

Lauren Grant is a professional culinary food scientist, food writer, recipe developer, and food photographer. Lauren is a previous magazine editor and test kitchen developer and has had work published in major national publications including Diabetic Living Magazine, Midwest Living Magazine, Cuisine at Home Magazine,,, and more.

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  1. Made this this past weekend for a friends dinner party and it was a HIT! So much flavor and the crunchy topping is spot on.