Almond Flour Thumbprint Cookies (Vegan + Grain-Free)

GFGluten Free

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These Almond Flour Thumbprint Cookies are Grain-Free, Vegan, Naturally Sweetened, and made with only 6 healthy ingredients!

You know those moments when you eat food that’s so good, you can’t help but do a little happy dance and close your eyes? Recipe testing these Almond Flour Thumbprint Cookies was one of those times for me.

Not only are they dance-party delicious, but they’re also Grain-Free, Naturally Sweetened, and made with only 6 healthy ingredients!

almond flour thumbprint cookies lined up on black wire cooling rack with gray background

So, what’s the secret to soft, pillowy cookies with crispy edges? In this case, it’s a combination of Almond Flour, Tapioca FlourAlmond Butter, and Maple Syrup…that’s pretty much it! The Almond Flour and Almond Butter give these cookies a great Almond flavor, but you can also add in a touch of Almond Extract if you’d really like to take things up a notch.

I wanted to keep these cookies on the healthier side, so I decided to fill them with some homemade Chia Seed Jam, which is also naturally sweetened! I made a Raspberry and Blueberry Jam for these cookies, but you can use any berry you’d like.

large white plate topped with almond flour thumbprint cookies with hand reaching for a cookie

These cookies are abso-freakin-lutely delicious, and are perfect for an afternoon pick-me-up, lighter dessert, or treat to share with friends and family! I love to warm mine up in the toaster oven and serve them with a tall glass of non-dairy milk. But now that I think of it, they’d also be great with some Tea or Hot Chocolate…

stack of almond flour cookies on white speckled plate with bite taken out of top cookie

A Few Final Thoughts:

  • If you don’t want to make your own Chia Seed Jam, you can always use store-bought! 
  • This Cookie dough is a little trickier to work with than a “standard” cookie recipe,  due to the use of different ingredients. Please read the instructions carefully – I’ve included lots of helpful tips too!
  • Also, it’s worth to note that the cookies change texture over time – if you eat them the day of baking, they will be crispy on the outside and soft on the inside. After around 8 hours, they get more soft and doughy. They are delicious either way, but just keep that in mind if you are planning on serving them a certain way! 

small white plate filled with almond flour thumbprint cookies

If you’re looking for more Vegan Cookie recipes, you’ll also love these Crunchy Vegan Gingerbread Cookies and these Flourless Tahini Sugar Cookies!

Finally, if you make this recipe and decide to share it on Facebook or Instagram, don’t forget to tag me @FromMyBowl + #FromMyBowl! I love seeing your delicious recreations 🙂


Almond Flour Thumbprint Cookies

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5 from 10 reviews

These Almond Flour Thumbprint Cookies are Grain-Free, Vegan, Naturally Sweetened, and made with only 6 healthy ingredients!

  • Author: Caitlin Shoemaker
  • Prep Time: 20 Minutes
  • Cook Time: 16 Minutes
  • Total Time: 36 minutes
  • Yield: 18-19 Cookies 1x
  • Category: Dessert
  • Method: Oven
  • Cuisine: American


  • 1/4 cup Unsalted Almond Butter
  • 1/2 cup Maple Syrup
  • 1/2 tsp Salt
  • 1 1/4 cup Fine Almond Flour
  • 1/2 cup Tapioca Flour/Starch
  • 1 tsp Baking Powder
  • Optional: 1/2 tsp Almond Extract (for an extra Almond flavor!)
  • 34 tbsp Chia Seed Jam


  1. Preheat the oven to 350F. Add the Maple Syrup, Almond Butter, Salt, and optional Almond Extract to a large bowl; whisk well, until the Salt has dissolved. Add the Almond Flour, Tapioca Flour, and Baking Powder to the same bowl, and use a spatula to mix the dough together until everything is evenly incorporated – the mixture will be a little wet/soft at this point.
  2. Place the final dough in the freezer for 10 minutes, to allow it to harden. In the meantime, grease or line 2 baking trays with parchment paper or a reusable silicone mat.
  3. Once the dough has hardened, use a small cookie scoop to take 2 tbsp of dough and round it into a ball; place the ball onto the baking tray, then press your thumb into the center of the dough. You do not need to spread the dough out further, as the cookies will spread in the oven! Add a heaping 1/2 tsp of Chia Seed Jam to the center of the cookie, then repeat with the remaining dough. (Note: As the dough spreads, I would suggest only baking 12 cookies per tray. If the dough starts to stick to your hands, get them a little wet!)
  4. Bake the cookies for 16-17 minutes, then remove from the oven. They will be soft when they first come out; let them sit on the baking tray for 5 minutes to harden, then carefully remove them with a spatula and transfer to a rack to let cool completely. Store leftovers at room temperature in a container with a loose fitting lid for up to 5 days.


  • I have not tested this recipe without Almond Flour and/or Tapioca Starch, and would not recommend substitutions.
  • Almond Butter may be replaced with another Nut/Seed Butter of choice
  • Chia Seed Jam may be replaced with another Jam or Jelly of choice

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These Almond Flour Thumbprint Cookies are Grain-Free, Vegan, Naturally Sweetened, and made with only 7 healthy ingredients! #vegan #almondcookies #grainfree #glutenfree #plantbased #cookies #thumbprintcookies #dessert | via

About the Author

Hey there, I’m Caitlin! I make easy-to-follow, wholesome, and budget-friendly vegan recipes that are mostly gluten-free and refined sugar-free. I’m also an avid yogi, love the great outdoors, am chocolate-obsessed, and enjoy eating almond butter straight off of the spoon.

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  1. These cookies are delicious and easy to make. I love that they are not only vegan but also healthy and gluten free. I added the almond extract which I enjoyed. They are a bit sweet for me but my family is sure to love them. Thank you Caitlin for recreating a family favorite we can all enjoy!

  2. Everyone I’ve given these cookies to has said they’re delicious! However I’ve found they’re a bit sweet for my taste, I’m going to tone down the maple a bit! Thanks for an awesome recipe again!!

  3. Wow. 10/10, will make again. So easy and delicious. Might have eaten all of them in two days. Amazing recipe, as usual!

  4. I make these every single year during Christmas time! These are so delicious and the consistency is chewy and soft, and slightly crunchy around the edges.

    I also use peanut butter because it’s cheaper and instead of tapioca starch, I use rice flour because I always have it at home. They turn out perfect every time 🙂

    Thanks a lot for this brilliant recipe.

  5. These are absolutely delicious with a wonder almond flavor. Love the chia jam recipe and its also something you could easily swap out for a different flavor of jam or even chocolate! Gonna be a new christmas cookie recipe!

  6. These are so good and so easy! My husband just asked me to make another batch so this is a winner!

  7. IM OBSESSED. These are so easy to make and taste incredible!! These are definitely a new staple in my house.

  8. Hi. I just made these. Taste great but had issue with them sticking to the pan. I didn’t note any direction to grease or paper the pan. What did I do wrong?

  9. These are too good. Very easy to make – I’m on my third batch because my husband and I ate all the ones I was supposed to bring over to my families. I love that it’s GF, my arthritis is so much worse when I eat lots of gluten or refined sugar.

  10. I made these and they are delicious! I want to make some for my sister but is sensitive to tapioca, is there anything I can substitute that for?

  11. I made these and they are delicious! I want to make some for my sister but she is sensitive to tapioca, is there any thing I can substitute the tapioca flour/starch for?