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Gluten-Free Thumbprint Cookies (Paleo)

Mar 15, 2025 · Leave a Comment

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Gluten-Free Thumbprint Cookies on a baking sheet and piled on a plate.
Gluten-Free Thumbprint Cookies on a baking sheet and piled on a plate.

These Gluten-Free Thumbprint Cookies are an easy, wholesome treat! You can use your favorite jam and even roll them in crushed nuts or coconut. This one-bowl recipe makes a lot so luckily they freeze well too.

And they’re also dairy-free, refined sugar-free and Paleo.

Dairy-free thumbprint cookies piled on a plate next to a cooling rack with more cookies on it.

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Why this recipe works

Thumbprint cookies are just the cutest kind of old-fashioned treat, aren’t they? Buttery cookies pressed in on the top (as if by someone’s thumb) and then filled with jam. Adorable.

But the classic version uses flour, butter and other ingredients some of us can’t tolerate. So I wanted to create a healthy thumbprint cookie (okay, maybe healthier) that everyone can enjoy.

So out goes the regular flour and instead we’re using almond flour, which is finely ground, peeled almonds. It retains the protein, fiber and healthy fats from the almonds, making it more nutritious than all-purpose flour. But because their natural oils can make baked foods a little greasy, we’re adding some arrowroot flour/starch (a fine powder similar to cornstarch) to make sure the cookies aren’t oily.

And because almond flour naturally contains moisture from its oil, we just need a bit of coconut oil to give the cookies a buttery texture without using butter (and without tasting like coconut).

Instead of refined white sugar, these almond flour thumbprint cookies uses honey as a sweetener. And they’re filled with a fruit-sweetened jam, making them refined sugar-free as well. I like to use apricot, raspberry or cherry jam, but use your favorite.

Just for fun, I like to roll some of them in either crushed pistachios, crushed pecans or unsweetened shredded coconut. They add color, texture and flavor but this step is completely optional.

And that’s how you make thumbprint cookies gluten free, dairy-free and Paleo!

What you need

The individual ingredients for Paleo thumbprint cookies in bowls with labels.

Ingredients:

  • 1 tablespoon coconut oil – You just need a little bit to give the cookies a buttery texture. Don’t use any more than this or they’ll be greasy.
  • ⅓ cup honey – This is just enough to make the cookies sweet but not too sweet.
  • 1 teaspoon vanilla extract
  • ¾ teaspoon almond extract (optional) – I like the extra almond flavor this adds but you don’t need to add it if you don’t want to.
  • 1 large egg, room temperature – If your egg is still cold from the fridge, submerge it in very warm water for 5 minutes.
  • 1¾ cups superfine blanched almond flour – This adds a great texture while also adding protein, fiber and healthy fats. Do not use almond meal.
  • ¼ cup arrowroot flour/starch – This helps dry out the almond flour a bit so the cookies aren’t oily.
  • ¼ teaspoon fine sea salt – Even desserts need a bit of salt to bring out the flavors.
  • ¼ cup fruit-sweetened jam – I like apricot, cherry or raspberry but use whatever flavor you like. Two of my favorite brands are St. Dalfour and Bionaturae (not ads, I just like them).
  • ¼ cup unsweetened shredded coconut, finely crushed pistachios or finely crushed pecans, for rolling (optional) – I like to roll some of the cookies in these coatings for flavor, texture and color but you don’t have to.

Equipment:

  • a microwave-safe large mixing bowl
  • a whisk
  • measuring spoons (<– I like the ones at this link because they fit into spice jars)
  • measuring cups
  • a measuring glass
  • a spatula (the kind for stirring, not flipping)
  • a fine-mesh sieve
  • a regular tablespoon or ice cream/cookie scoop with lever (I use a medium scoop/2 tablespoon/1 oz. scoop)
  • a round tablespoon measuring spoon or ½ tablespoon measuring spoon
  • parchment paper
  • 2 stainless steel baking sheets
  • cooling racks (optional)

How to make Gluten-Free Thumbprint Cookies

Step 1: In a large, microwave-safe bowl, add the coconut oil and microwave until melted, about 1 minute.

Step 2: To the coconut oil, add the honey, vanilla and almond extract (if using). Whisk until thoroughly combined. Add the egg and whisk again until combined.

Step 3: Place a sieve over the bowl and add half of the almond flour to the sieve. Sift it into the bowl, pressing through any hard clumps, and repeat with the rest of the almond flour. Remove the sieve and add the arrowroot and salt directly to the bowl. Stir with a spatula until completely combined.

Step 4: Chill the dough in the fridge for at least an hour or up to 2 days.

Step 5: When the dough is almost ready, heat the oven to 350° F.

Step 6: Line 2 baking sheets with parchment paper.

Step 7: Use a tablespoon or 2-tablespoon-sized cookie scoop and create about 2-tablespoon-sized balls of dough. If using the coatings (coconut, pistachios and/or pecans), roll the balls in the coatings. If the dough is sticking to your hands, get your palms slightly damp with water. Place the balls on the parchment-lined baking sheets (12 balls on each sheet). The cookies will spread a bit as they bake.

Step 8: Use the palm of your hand to just barely press the cookies down so they’re flat on top (don’t press too hard, you don’t want them to be too big or too thin). If the dough is sticking to your hands, get your palms slightly damp with water. Then use the bottom of a round tablespoon measuring spoon or ½ tablespoon measuring spoon to press into each cookie. Press down almost all the way. You want a somewhat wide and deep well in each cookie. If the dough is sticking to your spoon, get it slightly damp with water.

Step 9: Fill each cookie with ½ teaspoon jam (it helps to use the handle of a smaller measuring spoon to get the jam out). Don’t spread the jam out in the well – it’ll spread naturally.

Step 10: Bake the cookies on two racks in the oven for 10-12 minutes, rotating and swapping the sheets halfway through, until the cookies are golden brown around the edges of the bottoms. Let cool completely (on cooling racks, if using).

Healthy thumbprint cookies on a parchment paper-lined baking sheet.

Frequently Asked Questions (FAQ)

Can I make substitutions?

I know some people have success using finely ground sunflower seeds in place of almond flour to make recipes nut-free. I have not tried that with these cookies – if you do, please let me know how it goes.

You can use maple syrup in place of the honey.

You can use tapioca flour/starch in place of the arrowroot.

You can add the zest of a lemon or half an orange to the cookie dough for extra flavor.

Feel free to use your favorite jam. Cherry, apricot and raspberry all work well.

Can I make these Gluten-Free Thumbprint Cookies ahead of time?

Before rolling out the cookies, the dough can be refrigerated for at least an hour or up to 2 days.

Once the cookies are baked and cooled, you can keep them in the fridge for up to 5 days. They will get softer and chewier in the fridge.

Can I freeze these Gluten-Free Thumbprint Cookies?

To freeze them, roll out the cookies, place on a parchment-lined baking sheet, gently flatten them and add the well for the jam but don’t fill them with jam. Place in the freezer for at least 4 hours. Once the cookies are frozen through, transfer them to an airtight container and freeze for up to 3 months.

When ready to bake, transfer the frozen cookies to 2 parchment-lined baking sheets, fill with jam and proceed with the recipe. You might need to add 1-2 minutes to the cooking time but you might not, so check them at 10 minutes to be sure.

Are these also Paleo Thumbprint Cookies?

Yes. The recipe as written is Paleo-friendly.

Other recipes you might like:

  1. Paleo Chocolate Chip Cookies
  2. Paleo Shortbread Cookies
  3. Paleo Snickerdoodles
  4. Paleo “Oatmeal” Cookies
  5. Paleo Crumb Bars with Jam
Dairy-free thumbprint cookies piled on a plate next to a cooling rack with more cookies on it.

Gluten-Free Thumbprint Cookies (Paleo)

Don Baiocchi
These Gluten-Free Thumbprint Cookies are an easy, wholesome treat! You can use your favorite jam and even roll them in crushed nuts or coconut. This one-bowl recipe makes a lot so luckily they freeze well too.
And they're also dairy-free, refined sugar-free and Paleo.
No ratings yet
Print Recipe Pin Recipe
Prep Time 20 minutes mins
Cook Time 12 minutes mins
chilling time 1 hour hr
Total Time 1 hour hr 32 minutes mins
Course Dessert, Snack
Cuisine American
Servings 24 cookies
Calories 84 kcal

Ingredients
  

  • 1 tablespoon coconut oil
  • ⅓ cup honey
  • 1 teaspoon vanilla extract
  • ¾ teaspoon almond extract (optional)
  • 1 large egg, room temperature
  • 1¾ cups superfine blanched almond flour, not almond meal
  • ¼ cup arrowroot flour/starch
  • ¼ teaspoon fine sea salt
  • ¼ cup fruit-sweetened jam, such as apricot, raspberry or cherry
  • optional coatings: unsweetened shredded coconut, crushed pistachios, crushed pecans

Instructions
 

  • In a large, microwave-safe bowl, add the coconut oil and microwave until melted, about 1 minute.
  • To the coconut oil, add the honey, vanilla and almond extract (if using). Whisk until thoroughly combined. Add the egg and whisk again until combined.
  • Place a sieve over the bowl and add half of the almond flour to the sieve. Sift it into the bowl, pressing through any hard clumps, and repeat with the rest of the almond flour. Remove the sieve and add the arrowroot and salt directly to the bowl. Stir with a spatula until completely combined.
  • Chill the dough in the fridge for at least an hour or up to 2 days.
  • When the dough is almost ready, heat the oven to 350° F.
  • Line 2 baking sheets with parchment paper.
  • Use a tablespoon or 2-tablespoon-sized cookie scoop and create about 2-tablespoon-sized balls of dough. If using the coatings (coconut, pistachios and/or pecans), roll the balls in the coatings. If the dough is sticking to your hands, get your palms slightly damp with water. Place the balls on the parchment-lined baking sheets (12 balls on each sheet). The cookies will spread a bit as they bake.
  • Use the palm of your hand to just barely press the cookies down so they're flat on top (don't press too hard, you don't want them to be too big or too thin). If the dough is sticking to your hands, get your palms slightly damp with water. Then use the bottom of a round tablespoon measuring spoon or ½ tablespoon measuring spoon to press into each cookie. Press down almost all the way. You want a somewhat wide and deep well in each cookie. If the dough is sticking to your spoon, get it slightly damp with water.
  • Fill each cookie with ½ teaspoon jam (it helps to use the handle of a smaller measuring spoon to get the jam out). Don't spread the jam out in the well – it'll spread naturally.
  • Bake the cookies on two racks in the oven for 10-12 minutes, rotating and swapping the sheets halfway through, until the cookies are golden brown around the edges of the bottoms. Let cool completely (on cooling racks, if using).

Notes

Nutritional note: The nutrition info does not include the optional coatings (coconut, pistachios, pecans).
Substitutions
Feel free to use your favorite jam. Cherry, apricot and raspberry all work well.
I know some people have success using finely ground sunflower seeds in place of almond flour to make recipes nut-free. I have not tried that with these cookies – if you do, please let me know how it goes.
You can use maple syrup in place of the honey.
You can use tapioca flour/starch in place of the arrowroot.
You can add the zest of a lemon or half an orange to the cookie dough for extra flavor.
Make ahead
Before rolling out the cookies, the dough can be refrigerated for at least an hour or up to 2 days.
Once the cookies are baked and cooled, you can keep them in the fridge for up to 5 days. They will get softer and chewier in the fridge.
Freezer info
To freeze them, roll out the cookies, place on a parchment-lined baking sheet, gently flatten them and add the well for the jam but don’t fill them with jam. Place in the freezer for at least 4 hours. Once the cookies are frozen through, transfer them to an airtight container and freeze for up to 3 months.
When ready to bake, transfer the frozen cookies to 2 parchment-lined baking sheets, fill with jam and proceed with the recipe. You might need to add 1-2 minutes to the cooking time but you might not, so check them at 10 minutes to be sure.

Nutrition

Serving: 1cookieCalories: 84kcalCarbohydrates: 9gProtein: 2gFat: 5gSaturated Fat: 1gPolyunsaturated Fat: 0.05gMonounsaturated Fat: 0.1gTrans Fat: 0.001gCholesterol: 7mgSodium: 28mgPotassium: 62mgFiber: 1gSugar: 6gVitamin A: 10IUVitamin C: 0.3mgCalcium: 22mgIron: 0.1mg
Keyword almond flour cookies, almond flour thumbprint cookies, gluten free thumbprint cookies, paleo thumbrpint cookies
Tried this recipe?Mention @paleoglutenfreeguy or tag #paleoglutenfreeguy!

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Well hello there! I’m Don, the creator behind Paleo Gluten Free Guy. I share fun, vibrant recipes for good health and pure enjoyment. All of my recipes are gluten-free and the majority of them are also Paleo, meaning they’re free of grains, dairy, refined sugar and legumes.

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