These healthy chocolate thumbprint cookies have a buttery almond flavor, are gluten and grain free and guaranteed to please everyone!

In my family, the holidays are pretty much synonymous with indulging.

From Thanksgiving straight through to New Year’s there is food, food and more food.

And for me, while the filet or prime rib we typically have on Christmas is delicious and the stuffing my mom makes on Thanksgiving is out of this world amazing, I would gladly give it all up for a seat right in smack in the middle of the dessert table so I can stuff myself to the point of pain with all the sweet treats in front of me (and then of course roll over to the couch to moan in pain about how I shouldn’t have eaten so much for the next 2 hours).

Almond chocolate thumbprint cookies on a baking sheet next to a bowl of melted chocolate.
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Luckily for me and for all of my family, we’ve never had to deal with any dietary restrictions in the all-you-can-eat buffet that is the holidays.

But more and more, that seems to be the anomaly as plenty of adults and children are dealing with gluten intolerances and/or sensitives.

I can’t even imagine how hard holiday parties and get togethers become when you’re constantly worrying if there will be something you can eat at them.

So I wanted to make something that was gluten (and grain) free for all to enjoy as the holidays approach like these chocolate thumbprint cookies.

I know if it were me, I’d be most concerned about dessert (priorities, duh) so that’s exactly what I did.

There’s no reason these have to be for gluten free eaters only either. They’re a deliciously buttery (even though there’s no butter in them) and almond flavored (if you’re an almond lover you must try these pignoli cookies!) thumbprint cookie filled with chocolate…who wouldn’t love that?!

And if chocolate isn’t your thing (well then you’re crazy like my husband), fill them with any kind of jam you like.

The raspberry jam I use in these vegan thumbprints is always a good choice.

Or, a cranberry filled thumbprint like this cranberry orange thumbprint recipe would be so perfect for this time of year!

You can also try these paleo blueberry thumbprints or these tart cherry chocolate fudge thumbprints, both are gluten-free for all to enjoy!

Chocolate Thumbprint Cookie Ingredients

  • almond flour
  • ground flaxseed
  • baking soda
  • salt
  • brown sugar
  • egg whites
  • coconut oil
  • vanilla extract
  • almond extract
  • dark chocolate chips
Thumbprint cookies with chocolate spooned in the middle.

How to Make Healthy Thumbprint Cookies

Line a baking sheet with parchment paper and preheat the oven to 350 degrees.

Combine the flour, ground flax, salt, baking soda, and brown sugar in a large bowl.

In a small bowl, add the egg whites, extracts, and a tablespoon of coconut oil. Whisk together.

Pour the wet ingredients into the dry and mix just until combined.

Wet your hands a roll a tablespoon of dough for each thumbprint into a ball and place them on the baking sheet.

With the back of a wet 1/2 teaspoon, press down the center of each dough ball.

Bake for 12 minutes.

Take the cookies out of the oven and use the 1/2 teaspoon again to make the indent a little deeper. Allow the thumbprints to cool on a baking rack.

Melt the chocolate and coconut oil together in the microwave or on the stove top.

Spoon the chocolate into the indents of the cooled cookies and let them set for 10 minutes.

Tips and Substitutions

  • Chocolate: You can also use milk or dark chocolate if you choose.
  • Bob’s Red Mill has a super fine almond flour that is one of my favorites to use to use because it keeps a smooth texture. Especially since we are using ground flax in this recipe.
  • Almond extract and almond flour just go together for the best flavor, so don’t skip out on the extracts.
  • You can also roll the cookies in nuts for a little extra crunch. I do that for these chocolate cashew cookies and love the added texture.
  • Keep leftover chocolate thumbprint cookies in an airtight container for 5 days on the counter.

More Cookie Recipes To Try:

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5 from 1 vote

Almond Chocolate Thumbprint Cookies

Servings: 12 servings
Prep: 10 minutes
Cook: 12 minutes
Total: 22 minutes
Chocolate thumbprint cookies.
These chocolate thumbprint cookies have a buttery almond flavor, are gluten and grain free and guaranteed to please everyone!


  • 1 1/4 cup almond flour
  • 1/4 cup ground flaxseed
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1/4 cup brown sugar
  • 3 tablespoons egg whites
  • 1 tablespoon + 1/2 teaspoon melted coconut oil
  • 1/2 teaspoon vanilla extract
  • 1/4 teaspoon almond extract
  • 1/3 cup dark chocolate chips


  • Preheat oven to 350 degrees. Line a baking sheet with parchment paper or a silpat.
  • In a large bowl, combine the flour, flax seed, salt, baking soda and brown sugar.
  • In a small bowl, whisk together the egg whites, extracts and 1 tablespoon of the coconut oil.
  • Pour the wet ingredients into the dry and mix until combined.
  • With wet hands, roll about 1 tablespoon of the dough into a ball and place on the baking sheet.
  • Wet the back of a 1/2 teaspoon and gently press down in the center of each dough ball to create an indent.
  • Place the baking sheet in the oven and bake for about 12 minutes.
  • Remove from the oven and using the 1/2 teaspoon, press down again in the indent just to make it a bit deeper as it probably puffed up a bit while baking.
  • Let the cookies cool completely on a cooling rack.
  • Meanwhile, melt the chocolate chips and the 1/2 teaspoon coconut oil either in the microwave or on the stove top.
  • Once cookies are cooled, spoon the chocolate into the indent. Let them sit for about 10 minutes until set.
  • Store in an airtight container for up to 5 days.


Serving: 1SERVINGCalories: 123kcalCarbohydrates: 10gProtein: 4gFat: 8gSaturated Fat: 2gPolyunsaturated Fat: 6gSodium: 106mgFiber: 2gSugar: 7g

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American

Founder and Writer at Running to the Kitchen | About

Gina Matsoukas is an AP syndicated writer. She is the founder, photographer and recipe developer of Running to the Kitchen — a food website focused on providing healthy, wholesome recipes using fresh and seasonal ingredients. Her work has been featured in numerous media outlets both digital and print, including MSN, Huffington post, Buzzfeed, Women’s Health and Food Network.

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Recipe Rating


  1. Simple cookies with no big fuss, I loved it! Kids enjoyed baking with me and shaping cookies, thanks!