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Home ❯ Recipes ❯ Vegan Dessert Recipes

Gluten-Free Thumbprint Cookies

Lori standing in her kitchen.
Updated 11/20/2023 by Lori Rasmussen. This post may contain affiliate links.
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These healthy gluten-free thumbprint cookies are made with almond flour for a delightfully nutty, sweet, and wholesome treat. Only 6 ingredients, no eggs, dairy, or oil, and they're so much fun to make! They're a delicious after school snack, everyday dessert, or festive cookie for the holiday season! Plus, we've included tips for making your own jam!

thumbprint cookies filled with a variety of fruit-sweetened jellies.

I have very clear memories of eating Pepperidge Farm thumbprint cookies as a kid. Apricot was my favorite.

The buttery, slightly salty shortbread cookie combined with the slightly tart fruit jelly in the center...so good! Everyone loved those, right? I mean, I'm someone who chooses chocolate and vanilla desserts over fruity desserts 9 times out of 10, and even I loved them.

Now for the bad news. I just pulled up the Pepperidge Farm website to check the ingredients in their "Distinctive" Verona thumbprint cookies. Ugh, not good. Their ingredients include corn syrup, high fructose corn syrup, milk, egg, vegetable oils, etc.

That's why homemade (gluten-free and vegan) thumbprint cookies are the way to go!

close up of thumbprint cookie with orange jelly

Why You'll Love Them

Since almond flour has a rich, naturally buttery flavor, I thought it would be perfect for creating a more wholesome, oil-free and gluten-free thumbprint cookie.

Obviously the texture of these isn't exactly like a butter-filled, classic thumbprint cookie, but I'm okay with that because these have other perks! And I have a feeling you're going to love them, too.

It's so easy to switch up the flavors (and colors - the colors are half the fun!) with a variety of jams, jellies, or preserves.

For a refined sugar-free option, choose a store-bought, all-fruit jam, or make your own simple, naturally sweetened jam at home.

See the blueberry jam below? All you need are two ingredients and about 15 minutes to make it! It's seriously that easy. And the fruit flavor becomes SO concentrated and delicious.

Ingredients

  • almond flour - Currently I'm using this fine blanched almond flour by Nature's Eats, but any brand is fine. Almond flour is a key ingredients in the recipe and can't be substituted (at least not without more testing).
  • tapioca starch - This helps bind the cookies. Feel free to substitute a gluten-free flour blend.
  • sugar - I've tested these with regular sugar and coconut sugar. Other similar sweeteners should be fine, too.
  • maple syrup - Adds more sweetness, a bit of moisture, and nice flavor.
  • jam - Use your favorite jam, jelly or preserves - try strawberry, apricot, orange, raspberry, and blueberry! For refined sugar-free, choose a store-bought, all-fruit jam or make your own simple, naturally sweetened jam at home. More on this below!

See the recipe card below for amounts and full instructions.

quick homemade blueberry jam in a white bowl.

How to Make Jam for Thumbprint Cookies

In a small sauce pan combine 1 cup of frozen fruit such as blueberries, cherries, blackberries, or raspberries (chop larger pieces of fruit) with 1 tablespoon of sweetener (I used maple syrup). Bring just to a simmer, and cook over medium-low heat until thickened, about 10 minutes.

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Voila! You now have refined sugar-free jam! One cup of fruit will make a tad more than you need for these thumbprint cookies. Just store the leftover jam in the refrigerator, and enjoy it over the next few days.

How to Make Thumbprint Cookies

mixing the almond flour cookie dough.

The photo above shows what the cookie dough should look like after you've mixed the wet and dry ingredients together.

The dough should be very moist, slightly sticky, but not wet. If you accidentally add too much water, just mix in a bit more almond flour.

I used a small cookie scoop to measure out the dough, which makes it really easy to get uniformly sized cookies, but you can also use a tablespoon. Scoop up about 1.5 tablespoons of dough per cookie.

unbaked cookie dough on baking sheet.

Next, use your thumb to create an indentation in the center of each cookie. After the first impression with my thumb, I like to use my index finger to even it out. Fill it up with jam and bake. It's as simple as that!

Tip! These gluten-free thumbprint cookies don't spread during baking, so you'll probably be able to fit all of them on one small baking sheet.

thumbprint cookies filled with jelly and ready to be bakes.

The photo above is what the thumbprint cookies look like before going into the oven. And the photo below shows how they look when done.

oil-free vegan thumbprint cookies on a serving platter.

Thumbprint cookies are classic treat to share during the holidays, but I think they should be enjoyed year-round (especially when they're this healthy)!

I hope you enjoy these Gluten-Free Thumbprint Cookies. If you try the recipe be sure to rate it and comment below to let us know.

Oh, and if you're looking for more tasty dessert recipes with almond flour, be sure to try my Almond Flour Gingerbread Cookies and Almond Flour Brownies next!

On facebook or instagram? Share a photo of your healthy thumbprint cookies and tag @myquietkitchen so I can see!

More Vegan Gluten-Free Cookies

  • 3-Ingredient Almond Flour Cookies
  • Healthy Vegan Pecan Sandies
  • Oat Flour Peanut Butter Cookies 
  • Spiced Tahini Cookies
  • Oat Flour Double Chocolate Cookies
  • Cashew Butter Cookies

Recipe

A bite taken out of a strawberry thumbprint cookie resting on marble.

Gluten-Free Thumbprint Cookies (Vegan & Oil-free)

Author: Lori Rasmussen, My Quiet Kitchen
Healthy vegan gluten-free thumbprint cookies made with your choice of jam. They're oil-free, naturally sweetened, and made with just 6 ingredients!
4.94 from 16 votes
Servings: 14 cookies
Prep Time: 15 minutes mins
Cook Time: 18 minutes mins
Total Time: 33 minutes mins
Save on Pinterest Print Recipe

Equipment

  • parchment paper
  • cookie scoop (1.5 Tbsp)
  • baking sheet
(Keep screen awake)

Ingredients

  • 1 ½ cups almond flour (168 g) - Pack into measuring cup like you would when measuring brown sugar.
  • ⅓ cup tapioca flour (40 g) - Or GF flour blend
  • ¼ cup coconut sugar or other granulated sweetener
  • ¼ teaspoon fine sea salt
  • 3 tablespoons water
  • 1 teaspoon vanilla extract
  • 2 tablespoons maple syrup
  • approx. ¼ cup jam of choice - I used fruit-sweetened orange and raspberry storebought jam and a homemade, 2-ingredient blueberry jam (see Notes for recipe).

Instructions
 

  • Preheat oven to 350 degrees F, and line a baking sheet with parchment.
  • Combine the almond flour, tapioca, sugar, and salt in a mixing bowl. Whisk to combine.
  • In a mug whisk together the water, vanilla and maple syrup. Pour the wet mixture into the dry ingredients, and stir until fully combined.
  • The dough should be moist and holding together well but not wet. If it seems too moist, mix in a little more almond flour. With a small cookie scoop or a tablespoon, scoop up 1½ tablespoons of dough per cookie and place on cookie sheet. Use your thumb to make an indentation in the center of each cookie, and fill with jam.
  • Bake 16 to 18 minutes or until the bottoms are golden brown. The cookies will be soft right out of the oven but will firm up. Allow to cool on the baking sheet.

Notes

Storage
Store cookies at room temperature in a container with the lid not fully sealed (unless you don't mind the cookies getting soft) for 1 to 2 days, or refrigerate for up to 5 days. 
Easy 2-ingredient blueberry jam:
Combine 1 cup frozen wild blueberries and 1 tablespoon maple syrup in a small sauce pan. Simmer over low to medium-low heat until the berries have burst and the liquid has mostly evaporated. This should take about 10 to 15 minutes total.
Store leftover jam in the refrigerator for up to 4 days.

Estimated Nutrition (per serving)

Calories: 108kcalCarbohydrates: 12gProtein: 3gFat: 6gCholesterol: 0mgSodium: 44mgFiber: 1gSugar: 6g

Nutrition information is an estimate and will vary depending on the exact amounts and specific products and ingredients used.

Did you make the recipe?Comment below to share your feedback!

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    Recipe Rating




  1. Sue says

    August 08, 2025 at 4:25 pm

    Allergic to nuts. Can regular GF flour be used instead of almond flour?

    Reply
    • Lori Rasmussen says

      August 09, 2025 at 8:20 am

      Hi Sue - No, the fat content of almond flour is what makes these work. To use a gluten-free flour blend you'll need to add fat of some kind. I recommend following a recipe specifically written for the type of flour you'd like to use.

      Reply
  2. Sara says

    February 20, 2023 at 8:13 pm

    Is the tapioca required? I was thinking of using your 3-ingredient almond flour cookie recipe for these. Love the easy jam recipe.

    Reply
    • Lori says

      February 21, 2023 at 6:56 am

      Hi Sara, yes, the other almond flour cookie dough should work well for thumbprints, too.

      Reply
    • Robin Keane says

      December 17, 2024 at 7:24 pm

      I just made these cookies and they are delicious. Thank you for sharing. I was wondering if you can freeze them?

      Reply
      • Lori Rasmussen says

        December 18, 2024 at 12:49 pm

        Hi Robin - Glad you like them! The only concern with freezing will be the fruit/jam and it separating or being watery after thawing. You could definitely freeze the cookies before adding jam, though. And then thaw, fill, and bake briefly.

        Reply
  3. Andrea says

    October 09, 2021 at 6:54 pm

    Wow! Just wow! I made these and they are quick, easy, and delicious! I just found your web site and can’t wait to try more of your recipes! Thank you!

    Reply
  4. Evan says

    January 19, 2021 at 4:25 pm

    I made a triple batch a few weeks ago around Christmas. Excellent recipe!

    We were doing some socially distanced visiting because of COVID. So I made some of the cookies outside.

    I love your site. It's so great to have a high-quality source of baking recipes that are whole-food plant-based. It's not easy to find good oil-free baking recipes like you have on this site.

    Reply
    • Lori says

      January 21, 2021 at 7:50 am

      Thanks so much, Evan! I'm thrilled you enjoyed the cookies. That photo of you making cookies in the yard is great. Haha way to improvise! Thank you for being here. 🙂

      Reply
  5. job says

    May 07, 2020 at 3:42 pm

    Is there anything that could be substituted for tapioca flour that is a more common ingredient?

    Reply
    • Lori says

      May 08, 2020 at 7:29 am

      Corn starch is a pretty standard substitute for tapioca. I haven't tried it in these cookies, but it should work.

      Reply
  6. Bujji says

    May 03, 2020 at 5:05 pm

    Thank you. Just made them. Came out beautifully.

    Reply
    • Lori says

      May 06, 2020 at 6:55 am

      Wonderful, Bujii. So glad you liked them. 😀

      Reply
  7. Dahianne says

    October 03, 2019 at 5:55 pm

    They are amazing. I made them yesterday and just baked a double batch today.

    Reply
    • Lori says

      October 03, 2019 at 6:46 pm

      Wonderful! I'm so glad you're enjoying them. Thanks for the feedback, Dahianne!

      Reply
a photo of Lori Rasmussen in her kitchen.

Hi, I'm Lori!

I'm passionate about flavor and simplicity. I share vegan recipes with a focus on both!

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