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You are here: Home / Desserts / Almond Flour Apple Pecan Crisp (Gluten-Free)

Almond Flour Apple Pecan Crisp (Gluten-Free)

September 30, 2025 Updated: October 1, 2025 By Leanne Leave a Comment

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This Almond Flour Apple Pecan Crisp is filled with tender and juicy apples, warmly spiced with cinnamon and nutmeg, and baked under a thick, crunchy and buttery crisp topping. It’s a naturally gluten-free crisp made from old fashioned oats, almond flour and chopped pecans. The crisp topping is also made extra thick and bakes up super crunchy thanks to the melted butter. It’s made in a 9×13 pan so it’s the perfect fall dessert to feed a crowd. As a bonus, it can easily be made vegan by using plant-based butter!

Apple crisp on a plate with vanilla ice cream on top.

This recipe is 100% inspired by my almond flour peach crisp bars. I recently updated this recipe, and loved how the almond flour oat topping turned out, so I adapted it for this gluten-free apple crisp recipe.

It’s not your typical gluten-free crisp topping as it includes almost as much almond flour as oats, and also uses baking powder and cornstarch. I also opted to use melted butter instead of cutting in cold cubes of butter. This saves time and helps keep the crisp topping extra crisp!

Table of contents

  • Key ingredients and substitutions
  • How to make gluten-free apple crisp with almond flour
  • A note on measuring ingredients
  • Tips for making the best almond flour apple crisp
  • Recipe FAQs
  • More apple recipes

Key ingredients and substitutions

Below is a note on just a few of the ingredients. The recipe card at the end of this post includes all of the ingredients and the exact quantities used.

Ingredients to make apple crisp arranged individually.
  • Apples – You’ll need 3 pounds of apples for the filling, or 8 cups of chopped apples (about 8 medium-sized apples). I used Gala apples for this recipe as they’re sweet and hold their shape well. They’re also more affordable and readily available compared to some other varieties. If you prefer a more tart/sweet apple, Honeycrisp works well, and for even more tartness, use Granny Smith. If you use these varieties, you may wish to add a little more sugar to the filling.
  • Almond flour – My preference is to always use fine blanched almond flour but almond meal, which has a coarser texture, will also work in this recipe.
  • Oats – Old fashioned rolled oats (or large flake oats) are best for a crisp as opposed to quick oats, which are thinner. To keep this crisp gluten-free, make sure your oats are labelled as certified gluten-free.
  • Cornstarch – You’ll need cornstarch to help thicken the apples as they start to cook in the filling, but you’ll also need some for the crisp topping. This helps the topping stay tender while maintaining it’s crunchiness.
  • Pecans – For added crunch, the crisp topping includes 1 cup of chopped raw pecans. You can substitute with chopped raw walnuts or almonds if you prefer. Avoid using roasted or salted nuts as they burn quickly.

How to make gluten-free apple crisp with almond flour

Below is an overview of the steps to make this recipe along with photos. Refer to the recipe card at the end of this post for full recipe details.

Dry crisp ingredients stirred together in a glass bowl with melted butter and vanilla on the side.
Step 1: Stir together all of the dry ingredients for the crisp topping.
Crisp topping mixed together in a glass bowl with a fork.
Step 2: Add the melted butter and vanilla and stir together until well combined. Place in the fridge until ready to use.
Chopped apples and other filling ingredients in a large glass bowl.
Step 3: Peel, core and chop the apples into 1-inch pieces. Add them to a large bowl along with the other filling ingredients.
Apple filling spread out in white baking dish.
Step 4: Toss together until the apples are well coated. Spread them out into a 9×13 greased dish.
Crisp topping layered on top of apples in baking dish.
Step 5: Spread the oat pecan topping evenly over the apples.
Baked crisp cooling in dish.
Step 6: Bake at 350F for 20-25 minutes, or until the topping is golden brown. Remove from oven and carefully cover with foil. Bake for another 15-20 minutes, or until the filling is bubbling around the edges.

A note on measuring ingredients

For convenience, US cup measurements are included in the recipe card for this recipe. To ensure greater accuracy, however, weight and volume measurements are also provided. So, if you see grams (g), you’ll want to use a kitchen scale to weigh your ingredients, and if you see milliliters (ml), you’ll want to use a liquid measuring cup. Smaller quantities of ingredients are provided in teaspoons and tablespoons.

Tips for making the best almond flour apple crisp

  • Cut apples into even pieces. This will ensure the apples cook evenly. I like chunks of apples, so I recommend cutting the apples into 1-inch pieces. If you cut the apples smaller, they will cook quicker so you’ll need to reduce the baking time.
  • Cover with foil. The crisp topping browns quickly and the pecans burn easily, so you’ll want to cover the crisp with foil midway through baking.
  • Let the crisp sit. Once pulled from the oven, you’ll want to let the crisp rest for 15-20 minutes. This gives it time to set up and cool slightly before serving.
Apple crisp in baking dish with serving spoon and some scooped out on a plate to the side.

Recipe FAQs

Do you need to peel the apples for this recipe?

It’s not absolutely necessary, but I prefer to peel them as the skin can end up a little tough and chewy in the filling.

How can you make this recipe vegan?

Just substitute the butter with plant-based butter.

Can you use a different size dish?

This recipe makes a large apple crisp, so I recommend using a 9×13 baking dish or pan. If you’d like to use an 8 or 9 inch square pan or pie dish, just cut the recipe in half.

How do you store and reheat this crisp? Can you freeze it?

Any leftover crisp is best stored in an airtight container in the fridge. The topping will stay crisp for 3-4 days. You can reheat the crisp in the oven or warm individual servings in the microwave for 45-60 seconds. (The crisp topping will still be crispy!) You can also freeze the crisp, but I find the topping and apples don’t quite have the same texture once thawed and reheated.

Serving of apple crisp on a plate with melted ice cream on top.

More apple recipes

  • Almond Flour Apple Cake
  • Air Fryer Baked Apples
  • Apple Spice Cake with Buttercream Frosting
  • Apple Spice Muffins

If you make this recipe, I’d love to hear what you think in the comments below!

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Almond flour apple pecan crisp served on a plate with a spoon and scoop of ice cream.

Almond Flour Apple Pecan Crisp (Gluten-Free)

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  • Author: Leanne
  • Prep Time: 20 minutes
  • Cook Time: 45 minutes
  • Total Time: 1 hour 5 minutes
  • Yield: 8 servings
  • Category: Dessert
  • Method: Bake
  • Cuisine: American, Canadian
  • Diet: Gluten Free
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Description

This gluten-free Almond Flour Apple Pecan Crisp is filled with tender spiced apples and topped with a thick, crunchy and buttery oat topping.


Ingredients

For the crisp topping:

  • 1 3/4 cups (198g) old fashioned rolled oats
  • 1 1/4 cups (130g) fine blanched almond flour
  • 1 cup (130g) chopped raw pecans
  • 3/4 cup (171g) light brown sugar, packed
  • 2 tablespoons (15g) cornstarch
  • 1 teaspoon ground cinnamon
  • 1 teaspoon baking powder
  • 1/2 teaspoon fine sea salt
  • 1 teaspoon vanilla extract
  • 3/4 cup (170g) unsalted butter, melted

For the apple filling:

  • 3 pounds apples, about 8 medium-sized apples, peeled, cored and cut into 1-inch chunks (about 8 cups) *see note
  • 1/3 cup (80g) light brown sugar, packed
  • 2 tablespoons (15g) cornstarch
  • 1 tablespoon fresh lemon juice
  • 1 teaspoon vanilla extract
  • 1 teaspoon ground cinnamon
  • 1/2 teaspoon ground nutmeg
  • 1/4 teaspoon fine sea salt


Instructions

  1. Preheat oven to 350F and grease a 9 x 13 inch baking dish.
  2. In a large bowl, whisk together the oats, almond flour, pecans, brown sugar, cornstarch, cinnamon, baking powder and salt.
  3. Add the melted butter and vanilla and mix together until well combined. Place in fridge while you make the apple filling.
  4. In a large bowl, combine the chopped apples, brown sugar, cornstarch, lemon juice, vanilla, cinnamon, nutmeg and salt. Stir until the apples are well coated.
  5. Pour the apple mixture into the bottom of the prepared baking dish.
  6. Spread the oat topping over the apples in an even layer.
  7. Bake for 20-25 minutes, or until the topping is golden brown. Remove from oven and carefully cover the crisp with foil. Bake for another 15-20 minutes, or until the apple filling is bubbling around the edges.
  8. Let cool for 15-20 minutes before serving.

Notes

  1. I used Gala apples for this recipe as they’re sweet and hold their shape well. They’re also more affordable and readily available compared to some other varieties. If you prefer a more tart/sweet apple, Honeycrisp works well, and for even more tartness, use Granny Smith. If you use these varieties, you may wish to add a little more sugar to the filling.
  2. Cut the apples into even sized pieces so they cook evenly. I like big chunks of apples in my crisp, so I cut them into 1-inch pieces. If you cut the apples smaller, they will cook quicker so you’ll need to reduce the baking time.
  3. The crisp topping browns quickly and the pecans burn easily, so you’ll want to cover the crisp with foil midway through baking. 
  4. To keep this crisp gluten-free, make sure you use certified gluten-free oats.

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Filed Under: All Recipes, Almond Flour Recipes, Desserts, Gluten-Free, Holiday Recipes

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Meet Leanne

Hey there! I'm Leanne and welcome to Crumb Top Baking. I'm a self-taught baker, home cook and food photographer, and I'm passionate about sharing well-tested, simple and approachable desserts and savory recipes. Learn more about me and what you'll find on Crumb Top Baking....

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