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Mini Apple Pie Thumbprint Cookies

 November 10, 2020
A ceramic plate topped with the apple pie thumbprint cookies.

These Mini Apple Pie Thumbprint Cookies have a vegan shortbread base and a warm, vegan apple pie filling; pretty much the perfect cookie, and they are super easy to make. 

If you’ve been following me for a while, I think it’s pretty apparent that I have a thing for cookies. If cookies were a “love language,” they would be my primary one. Because of this deep cookie love, you can be sure that my cookies recipes are super tasty, and that they will be your go-to’s for many years to come!

I created these Apple Pie Thumbprint Cookies from my Paleo Raspberry Chia Thumbprint Cookie recipe, which so many of you love! I used the same short bread base, but just changed the filling. Instead of using raspberry chia jam, this time, I put together the perfect blend of apples, cinnamon, and maple syrup. And there you have it, warm apple pie thumbprint cookies!

Ingredients to make these Mini Apple Pie Thumbprint Cookies

As you can see from the ingredient list, you need only FIVE INGREDIENTS to make these cookies!!!! How cool is that?!? In fact, you probably already have everything you need to make these cookies. And if you don’t, a quick pit stop to your local grocery store will have everything you need.

  • Almond flour – For this recipe, you do need the almond flour. You could try other flours, but the consistency will be different. So, in order to get that shortbread texture, stick to the almond flour, because I know it works.
  • Coconut oil – I also love using coconut oil in this recipe. Just be sure to melt it! If you don’t like the taste of coconut oil, I recommend purchasing refined coconut oil. Refined coconut oil has a neutral aroma/taste, because it’s made from coconut meat that’s filtered and dried before being pressed into oil. On the other hand, unrefined coconut oil is made by from pressing fresh coconut meat – which means all that coconut flavor and smell stays in, as well as more of the nutrients, since the process doesn’t use heat or chemicals. So if you are a coconut lover, go with unrefined coconut oil. And, if you want to use butter or vegan butter instead of coconut oil, be my guest. You will still get a perfect result.
  • Maple syrup – The sweetener in this recipe is maple syrup, and the reason for that is simply because of it’s taste, which always screams fall! You will need maple syrup in both the shortbread cookie base and in the apple pie filling. If you prefer another sweetener, you can use it, just make sure it’s a liquid sweetener, so that your cookies don’t turn out dry.
  • Cinnamon – Cinnamon is definitely a key ingredient in apple pie, so yes! You need it in this recipe. You can also be adventurous and add some ground ginger, cloves, or even pumpkin pie spice.
  • Apples – Of course apples are the star of this recipe, and you only need two of them. You can use what ever apple variety you choose, but my go-to’s for this recipe are Honeycrisp, Jonagold, or even Braeburn.
  • Flaky sea salt (optional) – I always love sprinkling these apple pie thumbprint cookies with a pinch of flaky sea salt. It’s the best hint of flavor against the sweetness of the cookie. In fact, now that I am writing this out, I’m not sure why I called it an optional ingredient, because in my book, it’s mandatory!
A wire cooling rack, topped with the apple pie thumbprint cookies.

Instructions for making these Mini Apple Pie Thumbprint Cookies

To make these cookies, it couldn’t be easier. All you need to do is make the shortbread cookie dough base by mixing the base ingredients together in a bowl. Next, you chill the dough in the refrigerator. The reason for chilling the dough is so the coconut oil hardens, which makes it easier for these cookies to hold their shape, since we aren’t using an egg as a binder. 

While the dough is chilling, you make the apple pie filling. Clean the apples, and chop them up into tiny pieces. The smaller the better. Add the chopped apples and cinnamon to a small pan lightly coated with cooking spray (or oil), and then sauté them over medium-low heat for 3-5 minutes, or until the apples are tender. Transfer them to a small bowl to cool. Once the apples have reached room temperature, stir in the maple syrup. This ensures that the apples don’t get soggy and retain some texture.

When the dough is done chilling, line a baking sheet with parchment paper. Using a cookie scoop of your hands, form 8-10 cookies. They won’t spread much, so don’t worry if you pack them close together. Use the back of your thumb to gently press down into the center of each cookie. Fill each cookie with the apple pie mixture, and bake! That’s it.

Once they are out of the oven, sprinkle each one with flaky salt, and enjoy!

A sheet of parchment paper topped with the apple pie thumbprint cookies.

Other KALEJUNKIE thumbprint cookies that you don’t want to miss!

Paleo Raspberry Chia Thumbprint Cookies

Paleo Caramel Thumbprint Cookies

Peanut Butter Blossom Cookies

If you make these cookies, be sure to leave a rating and comment below! And of course, if you post them on Instagram, be sure to tag me so I can repost your beautiful creations!

Apple Pie Thumbprint Cookies by KALEJUNKIE

Mini Apple Pie Thumbprint Cookies

No ratings yet
Nicole Modic
Prep Time 15 minutes
Cook Time 10 minutes
Total Time 25 minutes
SERVES 8 mini cookies
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These mini paleo and vegan apple pie thumbprint cookies are made with only five ingredients and taste just like apple pie with a delicious shortbread cookie base. You will make this recipe for years to come!


Shortbread cookie base:

  • 1 ¼ cups almond flour
  • ¼ cup coconut oil melted
  • 2 tablespoons maple syrup
  • ½ teaspoon vanilla extract

Apple pie filling:

  • ¾ cup finely chopped apple this is about 2 medium-sized apples
  • 1 teaspoon cinnamon
  • 1 teaspoon maple syrup


  • Line a baking sheet with parchment paper.
  • In a medium bowl, whisk together the ingredients for the cookie base.
  • Chill the dough for at least 30 minutes.
  • And after the dough has been chilling for about 20 minutes, preheat your oven to 350.
  • Next, make the apple pie filling.
  • To make the apple pie filling, chop the apples into tiny pieces, and then add them, along with the cinnamon, to a small pan lightly coated with cooking spray (or a teaspoon of oil).
  • Saute the apples over medium-low heat for 3-5 minutes, or until the apples are tender.
  • Then transfer the apples to a small bowl to cool.
  • Once the apples have reached room temperature, stir in the maple syrup.
  • Form about 16 balls with the cookie dough, and use your thumb to gently make an imprint.
  • Spoon some apple filling into each cookie.
  • Bake for 10-12 minutes, or until the edges are golden.

Did you make this recipe?

I’d love to see what you made – tag @kalejunkie
in your posts and I’ll re-share!



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