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Thumbprint Cookie Recipe

Thumbprint Cookie Recipe – This jam-filled thumbprint cookie recipe is so easy to make and, as far as cookies go, its really not an unhealthful treat. Of course, that means that this recipe uses some very easy ingredient swaps from the classic thumbprint cookie recipe that is not so healthy.

thumbprint cookies recipe

Thumbprint Cookie Recipe Pairs Nicely with Tea

There is something therapeutic about making these cookies with a warm mug of tea. I think it has something to do with the fact they turn out looking so perfect and yet take such little effort. The steps are simple and the cookie is elegant fr such little time and ingredients.

I have really been enjoying Rooibos tea lately and there is nothing I love more in the afternoon than a nice cup of Rooibos tea with a thumbprint cookie. By the way, this tea is loaded with health benefits and is an amazing source of antioxidants.

Let’s get to the simple steps of how to make these thumbprint cookies with jam!

thumbprint cookies recipe

How to Make Jam-Filled Thumbprint Cookies

Making a quick batch of our jam-filled thumbprint cookies will not only taste good, but ensure you are eating whole foods that are healthy for you. Naturally, we have made some really great swaps in our ingredients from the classic thumbprint cookie.

I am pretty sure this thumbprint cookie is the most-frequently made sweet treat on our site. Once you combine the wet and dry ingredients to form your chocolate thumbprint dough, you’re halfway there. Follow these instructions:

how to make thumbprint cookies
how to make thumbprint cookies
how to make thumbprint cookies
how to make thumbprint cookies

Easy Swaps for Healthy Cookies

With just a few simple swaps, we can go from the butter-laded, sugar and brown sugar full and create this egg free, dairy free and gluten free delicious little cookie.

#1: Choose a whole grain gluten free flour

Over the years, I have experimented with three different whole grain flours, all of which work very well. And every time it comes down to the amazing whole grain, gluten free cup-for-cup replacement by King Arthur Flour. It’s the perfect whole grain flour blend for any of your other cookie recipes. Want to learn more about flour? Click here.

#2: All fruit jam filling

I love using Polaner All-Fruit brands which is Non-GMO. I typically choose either raspberry or strawberry jam, but you can try any flavor. If you do explore, leave a message in the comments for other recipe makers.

#3: Swap butter or shortening for coconut oil

The extra virgin coconut oil is used in place of butter or shortening. If you’ve never baked with coconut oil, you must give it a try. It’s a one-for-one swap with butter and leaves a crisp cookie on the outside while soft on the inside.

#5: Sweetened with maple syrup

Sweetened with “whole food” maple syrup, which keep our thumbprint cookies free from added refined sugar!

thumbprint cookies recipe

A little tip about maple syrup:

When you’re sourcing maple syrup, be sure to look for organic, pure maple syrup. Did you know pure maple syrup is actually NOT a refined sugar? It comes directly from the sap of the maple tree and contains antioxidants and phytonutrients. Click HERE to learn more about the benefits of pure maple syrup.


Thumbprint Cookie Recipe

This jam-filled Thumbprint Cookie recipe is gluten free, dairy free, egg free and sweetened naturally. Delicious and easy to make!

thumbprint cookies recipe
Save Recipe
  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Total Time: 30 minutes
  • Yield: 18 1x


  • 1 cup almond flour or finely ground cashew flour
  • 1 1/2 cups gluten free flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon sea salt
  • 1/2 cup pure maple syrup
  • 1/3 cup organic coconut oil, melted
  • 1 teaspoon pure vanilla extract
  • 1 teaspoon almond extract

Jam Filling:

  • 1/3 cup all-natural jam
  • 1 teaspoon lemon juice


  1. Preheat oven to 350 degrees. Line two large baking pans with unbleached parchment paper or use a non-toxic baking stone.
  2. In a large bowl, add the almond flour, gluten free flour, baking powder, and salt. Whisk to combine.
  3. Pour in the maple syrup, melted coconut oil and vanilla extract (and almond extract, if using) and combine with a wooden spoon or hand-mixer for about 2-3 minutes until a dough begins to form. Knead with your hands if the dough is not forming.
  4. Using a small scoop or medium scoop, scoop the dough and place it on the baking pan about 2 inches apart. Roll each scoop into a ball.
  5. Using a moist 1/4 – 1/2 teaspoon, push the teaspoon into the center of each dough ball and set aside.
  6. In a small bowl, combine the all-fruit jam and lemon juice and mix until well combined. Add approximately 1/2 teaspoon of jam per cookie.
  7. Place the cookies in the oven and bake for 10-12 minutes. Remove cookies from the oven and let cool slightly.

Last Step! If you loved our recipe, leave us a review below. This helps future recipe makers and ensures continued high-quality recipes for years to come!

© 2024 clean cuisine Recipe by:

Aimee Niedosik

Aimee loves to craft delicious, nutrient-dense recipes to share with her family and friends. While in remission from autoimmune diseases and underlying viruses, she still maintains an anti-inflammatory and anti-aging diet. Aimee is a Christian, website designer, autoimmune community leader and lives in North Carolina with her husband, 2 kids and 2 dogs.

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Wednesday 22nd of March 2023

Aimee,, I am sensitive to Almonds and Cashews, is there such thing as Pecan flour or macadamia nut flour?? The only two nuts i’m not sensitive to??

Aimee Niedosik

Wednesday 22nd of March 2023

Hi Sherry, In this case, I would substitute with more gluten free flour to replace the almond flour!

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