Gluten-Free Apple Pecan Crisp with Almond Flour

This Almond Flour Apple Pecan Crisp features tender, juicy apples spiced with cinnamon and nutmeg, baked under a thick, crunchy, buttery crisp topping. Naturally gluten-free, the topping combines old-fashioned oats, almond flour and chopped pecans. Using melted butter yields an extra-crunchy finish and a sturdy, scoopable topping. Baked in a 9×13 pan, this crisp is a perfect crowd-pleasing fall dessert. It can easily be made vegan by substituting plant-based butter for the butter.

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

This recipe is adapted from an almond flour peach crisp bars recipe. I updated the oat-and-almond topping and found it worked beautifully as a gluten-free apple crisp topping. It’s not a typical crisp topping — there’s nearly as much almond flour as oats and the mixture includes baking powder and cornstarch for structure and tender crunch. Melting the butter rather than cutting in cold cubes shortens prep time and encourages a uniformly crisp texture.

Key ingredients and substitutions

Below are notes on a few important ingredients. The full ingredient list with quantities appears in the recipe card further down.

Ingredients to make apple crisp arranged individually.

Apples: Use 3 pounds (about 8 medium apples) peeled, cored and chopped into roughly 1-inch pieces (about 8 cups). Gala apples work well because they’re sweet and hold their shape. For a sweeter-tart balance try Honeycrisp, or use Granny Smith for a more tart result — you may want to increase the sugar slightly with tart varieties.
Almond flour: Fine blanched almond flour is preferred for a light texture; almond meal with a coarser grind can be used if that’s what you have.
Oats: Old-fashioned rolled oats (large flake) are best for a crisp topping; quick oats are thinner and won’t produce the same texture. To keep the recipe gluten-free, choose certified gluten-free oats.
Cornstarch: Cornstarch helps thicken the apple filling as it cooks and also keeps the topping tender while allowing it to stay crunchy.
Pecans: The topping includes 1 cup chopped raw pecans for extra crunch. Substitute raw walnuts or almonds if preferred. Avoid roasted or salted nuts, which can burn in the oven.

How to make gluten-free apple crisp with almond flour

This overview highlights the major steps. Full, precise measurements and timing are listed in the recipe card below.

Dry crisp ingredients stirred together in a glass bowl with melted butter and vanilla on the side. — **Step 1:** Whisk together oats, almond flour, chopped pecans, brown sugar, cornstarch and spices for the topping.

Crisp topping mixed together in a glass bowl with a fork. — **Step 2:** Stir in melted butter and vanilla, then chill the mixture briefly while preparing the apples.

Chopped apples and other filling ingredients in a large glass bowl. — **Step 3:** Peel, core and chop apples into uniform 1-inch pieces. Toss them with the filling ingredients so they are evenly coated.

Apple filling spread out in white baking dish. — **Step 4:** Spread the apple mixture in a greased 9×13-inch baking dish.

Crisp topping layered on top of apples in baking dish. — **Step 5:** Distribute the oat-pecan topping evenly over the apples.

Baked crisp cooling in dish. — **Step 6:** Bake at 350°F until the topping is golden, then tent with foil and continue baking until the filling bubbles at the edges. Let cool briefly before serving.

A note on measuring ingredients

The recipe card includes US cup measurements and also metric weights for accuracy. Use a kitchen scale when grams are provided. Milliliters indicate liquid measure. Smaller amounts are given in teaspoons and tablespoons.

Tips for making the best almond flour apple crisp

Cut apples evenly. Even pieces ensure uniform cooking. I recommend 1-inch chunks for a substantial bite; smaller pieces will cook faster and require less oven time.
Cover with foil halfway through baking. The topping browns quickly and nuts can scorch, so tent the dish with foil after the topping is golden.
Let it rest. Allow the crisp to sit 15–20 minutes after baking so the filling sets and is easier to serve.

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?

Peeling is optional, but I prefer to peel them because apple skin can become a little tough or chewy in the filling.

How can you make this recipe vegan?

Substitute plant-based butter for the butter. Alternatively, use an oat-only topping to make the crisp fully vegan; increase the oat topping quantities to cover a 9×13 dish if using a smaller recipe.

Can you use a different size dish?

This recipe fills a 9×13 pan. If you prefer an 8 or 9-inch square pan or a pie dish, halve the recipe.

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

Store leftovers in an airtight container in the refrigerator; the topping stays crisp for 3–4 days. Reheat in the oven or microwave short bursts. You can freeze the crisp, but reheated texture may be softer than fresh-baked.

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

If you make this recipe, please leave a comment to share how it turned out — I love hearing reader feedback and adaptations.

Recipe

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

Almond Flour Apple Pecan Crisp (Gluten-Free)

A gluten-free almond flour apple pecan crisp with tender spiced apples and a thick, crunchy oat-pecan topping.

Prep Time: 20 minutes | Cook Time: 45 minutes | Total Time: 1 hour 5 minutes | Servings: 10

Author: Leanne Combden

Ingredients

For the crisp topping:

1 ¾ cups old fashioned rolled oats (198 g)
1 ¼ cups fine blanched almond flour (130 g)
1 cup chopped raw pecans (130 g)
¾ cup light brown sugar, packed (170 g)
2 tablespoons cornstarch (15 g)
1 teaspoon ground cinnamon
1 teaspoon baking powder
½ teaspoon fine sea salt
1 teaspoon vanilla extract
¾ cup unsalted butter, melted (170 g) — or plant-based butter to make vegan

For the apple filling:

3 pounds apples (about 8 medium), peeled, cored and cut into 1-inch chunks (about 8 cups)
⅓ cup light brown sugar, packed (80 g)
2 tablespoons cornstarch (15 g)
1 tablespoon fresh lemon juice
1 teaspoon vanilla extract
1 teaspoon ground cinnamon
½ teaspoon ground nutmeg
¼ teaspoon fine sea salt

Instructions

Preheat oven to 350°F and grease a 9×13-inch baking dish.
In a large bowl, whisk together the oats, almond flour, pecans, brown sugar, cornstarch, cinnamon, baking powder and salt.
Add melted butter and vanilla; mix until combined. Chill while preparing the filling.
In a large bowl, combine chopped apples, brown sugar, cornstarch, lemon juice, vanilla, cinnamon, nutmeg and salt; stir until the apples are evenly coated.
Pour the apple mixture into the prepared baking dish and spread into an even layer.
Spread the oat topping over the apples in an even layer.
Bake 20–25 minutes, or until the topping is golden brown. Remove from oven and carefully tent with foil, then bake another 15–20 minutes, or until the filling bubbles at the edges.
Let cool 15–20 minutes before serving.

Notes

Gala apples hold their shape and provide natural sweetness. For more tartness, use Granny Smith and consider adding a touch more sugar.
Cut apples into even pieces so they cook uniformly. Smaller pieces will cook faster and require less baking time.
Because the topping browns quickly and pecans can burn, tent the dish with foil after the topping has browned.
Use certified gluten-free oats to maintain a gluten-free dish.

Nutrition (per serving, estimate)

Nutrition information is an estimate and will vary with substitutions and brand choices.