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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: 1/6 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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