Tender, moist, sweet almond flour apple pie cookies are the perfect healthy fall treat. They’re loaded with moreish cinnamon apple pie filling over nutrient-dense pumpkin almond flour cookie dough for healthy mini apple pies that are vegan, grain-free, gluten-free, oil-free, egg-free, and refined sugar-free!

Sweet and Simple Almond Flour Apple Pie Cookies
Truthfully, I never feel the need to wait until fall to enjoy sweet and cozy cinnamon apple pancakes, apple crisp, and caramel apple cheesecake. However, with the addition of almond flour and pumpkin purée in the cookie dough and a jammy apple pie topping, these vegan apple pie cookies are a wonderful, bite-sized fall treat (and equally delicious as an apple pie)!
Regular cookies are often loaded with refined ingredients and empty calories, though, and I’m trying to reduce my consumption of both. Luckily, this apple pie cookie recipe uses ingredients that create great texture and flavor (wonderfully moist and tender with apple pie flavor), are naturally gluten-free and vegan, and create a surprisingly nutrient-packed treat.
In fact, these soft apple cookies contain plant-based protein, healthy fats, fiber, several micronutrients, and can be made low-carb, too! I mean, what could be better than healthy bite-sized apple pie cookies? Maybe the fact that this recipe also only requires minimal hands-on prep, too?!
Plus, these healthy cookies are a great addition to fall potlucks and parties, alongside gluten-free, vegan snickerdoodles, gingerbread cookies, raspberry thumbprints, or pumpkin cookies!

The Ingredients
The recipe for these vegan apple cookies is made entirely from common pantry staples in most gluten-free and/or vegan baker kitchens. Meaning, you may not even require a trip to the grocery store.
The Cookie Dough
- Almond flour: Use super-fine or fine almond flour (ground blanched almonds). I don’t recommend using almond meal, as the soft mini apple pies will be mealy/crumbly and more prone to falling apart.
- Tapioca flour: When combined with almond flour, tapioca flour will add lightness and help with browning.
- Sugar: I used coconut sugar, but any granulated sugar, like organic brown sugar, date sugar, white sugar (if that’s all you have at home), etc., will work for these caramel apple cookies.
- Baking powder: This helps keep the almond flour cookies from becoming too dense or spreading.
- Pumpkin purée: Use homemade or store-bought canned pumpkin purée, NOT pumpkin pie filling, to add moisture and bind these vegan apple cookies.
- Vanilla extract: Use natural vanilla, when possible, to avoid an artificial aftertaste.

Apple Pie Filling
- Apple: Use a crisp apple, as sweet or sweet-tart as you’d like. I.e., Honey Crisp, Gala, Pink Lady, Jonagold, Granny Smith apples, etc.
- Coconut sugar: Coconut sugar is unrefined and has a caramel flavor that pairs wonderfully with cinnamon and apples. Brown sugar or a sugar-free brown sugar substitute would also work well.
- Dairy-free milk: Use any unsweetened non-dairy milk. I.e., almond milk, coconut milk, cashew milk, etc.
- Cornstarch: (or tapioca starch) to thicken the apple pie cookie filling.
- Lemon juice: To balance and brighten the filling flavors.
- Cinnamon: For even more warming depth, use apple pie spice or pumpkin pie spice (which contains several warming spices like cinnamon, nutmeg, cloves, ginger, etc.).
- Salt: To balance and enhance flavors within the diced apple pie filling.

Optional Add-ins
- Coarse sugar: Like turbinado sugar (raw cane sugar). Roll each dough ball in it before shaping and filling for extra sweetness and crunch once baked.
- Chopped nuts: Like walnuts/ pecans, to sprinkle over the mini apple pies for crunch.
- Dried fruit: A handful of raisins, cranberries, or chopped dates could all be added to the apple filling for extra sweetness.
- Glaze: Combine maple syrup or water and powdered sugar to make a glaze.
- Salted caramel: To drizzle over the apple spice cookies.
Please read the recipe card below for the full ingredients list, measurements, complete recipe method, and nutritional information.

How to Make Caramel Apple Pie Cookies?
- First, add all the cookie dough dry ingredients (almond flour, tapioca flour, sugar, and baking powder) to a bowl and stir.
- Then, add the pumpkin purée and vanilla extract and mix it with your hands until a dough forms.
If the mixture is too sticky, add more almond flour, a spoonful at a time.
- Roll the dough into a ball and wrap it in clingfilm to chill in the fridge for 30 minutes. This allows the dough to firm up and become easier to work with.

- Meanwhile, finely dice the apples, and add all the apple pie filling ingredients to a saucepan. Bring the mixture to a boil, stirring frequently, then reduce the heat to low and allow it to simmer for about 3 minutes.

- Then, preheat the oven to 360 °F/180 °C and line a baking sheet with parchment paper or a silicone mat.
- Divide the chilled cookie dough into 9 pieces (estimating or using scales for accurate results) and roll each piece into a ball. Then, evenly spread them across the prepared tray, with space in between.

- Press an indent carefully into each of the cookie dough balls using the back of a 1-teaspoon measuring spoon. Then, use your fingers to gently widen it until the cookie is entirely bowl-like, with a small lip around the edge (to hold the filling).
Refer to the step-by-step images or video for more guidance. They should look a little like a mini pie crust shape.

- Divide the diced apple pie filling between the cookies and then transfer them to the oven for 15-20 minutes. Once ready, remove them from the oven and allow them to cool on a wire rack, then enjoy!
To take these apple spice cookies to the next level, drizzle them with some vegan salted caramel sauce when serving. Alternatively, gently warm one in the microwave and serve it with a small scoop of vegan vanilla ice cream.

Storing Instructions
Make ahead: You can prepare the filling three days in advance and the cookie dough 5 days in advance, and store them separately, covered in the fridge. Alternatively, 2-3 months in the freezer for the cookie dough (in plastic wrap) should also work.
Store: Allow the vegan apple cookies to cool and then store them in an airtight container at room temperature for a day or two or in the fridge for up to 5 days. The filling will make the cookies soften over time, so they’re best on days one and two.
Freeze: Spread the apple pie cookies across a baking tray, not touching, and freeze until solid. Then transfer them to a freezer bag for up to 3 months. When you want one, allow it to thaw on the kitchen counter until ready to enjoy.

FAQs
Can I use homemade pumpkin purée?
Homemade pumpkin purée can have a wetter moisture content than canned purée, so you may need to add an extra spoonful or two of almond flour.
Could I substitute the pumpkin purée?
It’s possible to use mashed sweet potato or butternut squash for the closest flavor match, though they may not bake exactly the same. Applesauce is one replacement I use in baking a lot that should work well in this apple cookies recipe. Mashed banana could also work, though the flavor is fairly strong.
Can I substitute any other flour?
I haven’t tried these caramel apple pie cookies with anything other than almond flour. However, cashew flour has similar properties, so should bake similarly. Sunflower seed flour is your best bet for a nut-free version, though the flavor is more robust.

Recipe Notes and Top Tips
- Sweeten to taste: Depending on how sweet or tart the apples are, sweeten the apple pie filling to taste.
- Allow them to cool: These gluten-free almond flour pumpkin cookies will be crumbly and tender right out the oven, and the filling will be scaldingly hot. Allow them to cool to firm up.
- Adjust the texture: I’ve diced the apples to still be fairly chunky in the filling. Dice them even smaller for a more tender, less chunky filling.
More Vegan Fall Bakes
- Pumpkin chocolate no-bake bars
- Easy apple strudel
- The best vegan pumpkin pie
- Vegan apple muffins
- Pumpkin chocolate chip bread
- Pecan tarts (vegan butter tarts)
- Healthy gluten-free pecan pie
If you try this delicious vegan apple pie cookie recipe, I’d love a comment and ★★★★★ recipe rating below. Also, please don’t forget to tag me in re-creations on Instagram or Facebook with @elavegan #elavegan—I love seeing them.

Apple Pie Cookies
Video
Ingredients
Cookie Dough
- 1.5 cups (160 g) almond flour
- 5 Tbsp (40 g) tapioca flour (see notes)
- 6 Tbsp (60 g) coconut sugar (see notes)
- 1 tsp baking powder
- ⅓ cup (80 g) pumpkin puree
- 1 tsp vanilla extract
Apple Filling
- 1 apple diced
- 3 Tbsp (30 g) coconut sugar
- ¼ cup (60 ml) dairy-free milk
- 1 ½ tsp lemon juice
- ½ tsp cinnamon
- ⅜ tsp cornstarch
- 1 pinch of salt
Instructions
- You can watch the video in the post for visual instructions.First, add all the cookie dough dry ingredients (almond flour, tapioca flour, coconut sugar, and baking powder) to a bowl and stir.
- Then, add the pumpkin purée and vanilla extract and mix it with your hands until a dough forms.If the mixture is too sticky, add more almond flour, a spoonful at a time.
- Roll the dough into a ball and wrap it in clingfilm to chill in the fridge for at least 30 minutes.
- Meanwhile, finely dice the apples, and add all the apple pie filling ingredients to a saucepan. Bring the mixture to a boil, stirring frequently, then reduce the heat to low and allow it to simmer for about 3 minutes.
- Preheat the oven to 360 °F/180 °C and line a baking sheet with parchment paper or a silicone mat.
- Divide the chilled cookie dough into 9 pieces (estimating or using scales for accurate results) and roll each piece into a ball. Then, evenly spread them across the prepared tray, with space in between.
- Press an indent carefully into each of the cookie dough balls using the back of a 1-teaspoon measuring spoon. Then, use your fingers to gently widen it until the cookie is entirely bowl-like, with a small lip around the edge (to hold the filling).Refer to the step-by-step images or video in the post for more guidance.
- Divide the apple pie filling between the cookies and then transfer them to the oven for 15-20 minutes. Once ready, remove them from the oven and allow them to cool on a wire rack, then enjoy!
Notes
- Tapioca flour: Any other starch such as arrowroot etc. might work too.
- Coconut sugar: You can use any other granulated sugar, such as organic brown/white sugar, date sugar, etc.
- The total time doesn't include chill time.
Nutrition information is an estimate and has been calculated automatically




I made these with apple sauce, they are so delicious and easy to make.. Thank you for all your wonderful recipes 🩷🙏🏼
So happy you liked them, Ofira! 😊 Thanks so much for trying the recipe and for your kind feedback. 💛
Hello again! Can I made the dough the day before and put it in the refrigerator instead of the freezer? Thank you!
Yes, Mandana, I actually answered your question already in the blog post:
My apologies! Thanks again
No worries at all. 🙂
Will it taste good without the apple filling? Last time I made something similar, my preschool students didn’t like the apple filling part.
They still taste fine without the apple filling but the apple filling definitely makes them better.
The cookie base is soft, sweet, and a little cakey thanks to the pumpkin purée, so you can bake them as plain pumpkin cookies and they will turn out yummy.
If you want to keep the little “indent” shape, you can also fill them with:
• a tiny bit of chocolate spread
• a small spoon of jam
• a dot of nut/seed butter
Hello, if I dice the apples very finely and only use a small amount in the pie, should I reduce the other ingredients in the apple filling?
Hi Mandana! If you’re only using one small, finely diced apple, you don’t need to reduce most of the other ingredients. The filling should still work well as written.
The only thing you might adjust is the dairy-free milk:
Use 2–3 tablespoons milk instead of ¼ cup, since less apple means less natural moisture.
Everything else can stay the same.
The sugar, cinnamon, cornstarch, and lemon juice all help create flavor and thickness — even with a smaller amount of apple.
May I use fresh lemon? Or does it taste better with store bought lemon juice? How long does it take to cook the apples? Thank you
Yes, you can definitely use fresh lemon juice — it tastes even better than store-bought. 🍋
For the apples, just simmer them for about 3–4 minutes until they’re slightly soft and the sauce thickens a bit. You don’t want them mushy, just tender enough to blend nicely with the cookies.
I’m a bit lost with the quantity of cornstarch.. 3/8 tsp? If I measure 1/4 tsp will it be ok?
PS They look really delicious!
Hi Maria, you can use a heaped 1/4 tsp. 🙂
Enjoy!
Hello!
Should I use One 1/4 teaspoon + one 1/8 teaspoon of cornstarch. to get 3/8 tsp?
I don’t have 3/8 tsp.. Thank you
Yes, exactly! 😊 One ¼ teaspoon + one ⅛ teaspoon of cornstarch equals ⅜ teaspoon!
Just made this today for a family baking competition and lets just say I won 🙂 sooo delicious!
That is fabulous! Thanks so much for leaving a comment and review! 🙂
I made these today. Delicious! I did double the apple filling and used almost all of it My cookies were a touch under 3 inches in diameter.. Thank you!
You are very welcome, Jill! Thanks for your feedback. 🙂
This was amazing!
I ve been looking for some delicious tart like this for a while. our daughter is celiac and we are always falling short in the treat department. This was so delicious and the almond flour add a beautiful texture and flavour. Daughter loved it too! it’s a great treat to take for her to someone’s birthday party if the cake isn’t safe for her to eat.
So happy to hear she liked it! Thanks for your feedback. 🙂
Hello. Almond flour is high in fat… can I use oat flour instead? These cookies look incredible, great idea!
It’s healthy fat and nutrient dense. No, I do not recommend oat flour.
Can you freeze these if you make a double batch?
You can! Check the storing instructions in the blog post. 🙂
Hay diferencias entre harina y almidón de tapioca. Es almidón o harina? Gracias
In the US, there is no different. It’s almidón (starch).
Is the crust crunchy or soft?
It’s rather soft! 🙂
looks like much more than 1 apple..re pumpkin puree: is it canned or homemade? thanx in advance.
Hi Dina, no, I used just 1 apple, not more. Used homemade pumpkin puree.
Hello what can i substitute for pumpkin puree it’s sweet potato ok?thank you🙂
Hi Lucia! Yes, that should be fine! 🙂
Thank you!