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Paleo Blueberry Thumbprints

These paleo blueberry thumbprints combine a soft chewy cookie and a slightly sweet fruity blueberry filling for a healthy grain free dessert you’ll love.

You know the question “if you had to pick one food to eat on a deserted island, what would it be?” or some derivation thereof that people like to ask all the time in those random hypothetical situations that will never actually happen?

Yeah, I hate that question.

I literally just cannot answer it.

Paleo Blueberry Thumbprints

I mean there’s pizza, pasta, rare steak (omg how could I give that up?), cheese… I could go on and on and on.

I’ve stopped even trying to think about it when that question arises anymore and just say “I don’t know, stop asking dumb questions like that” and move on.

Ask me to pick one kind of cookie to eat for the rest of my life though, and hands down, without hesitation, it’d be a thumbprint.

And if not these blueberry thumbprints, then these cranberry orange thumbprint cookies made with almond pulp or these classic vegan thumbprint cookies.

Paleo Blueberry Thumbprint cookies

Thumbprints are like the king of the dessert world because they’re basically a cookie-pie love child and how can you go wrong with that?

I know some people might be all “but you’re not picking something with chocolate?!” in an outraged state, but as much as I love a good piece of dark chocolate, thumbprints still win the stupid hypothetical food question award.

Of course, there’s always these almond chocolate thumbprints for that situation too.

There’s just something about the combination of a sweet fruit filling and a chewy cookie crust that puts them out in front.

Granted, you could always do a chocolate thumbprint cookie base like in these tart cherry fudge thumbprints and then boom, best of both worlds.

Grain Free Blueberry Thumbprints

These paleo blueberry thumbprints happen to be pretty good for you too considering they’re grain, gluten and dairy free so no worries about how you’d look in your eternal bathing suit attire when you’re stranded on that deserted island eating them 24/7 either.

Just lookin’ out for ya.

Blueberry thumbprint cookies.

Paleo Blueberry Thumbprints

Paleo blueberry thumbprints are a chewy cookie with a magical blueberry filling. And pretty good for you!
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Prep Time 15 minutes
Cook Time 12 minutes
Total Time 27 minutes
Servings 10 servings


For the Filling

  • 2 cups Blueberries
  • 1 tablespoon Pure Maple Syrup
  • 1 tablespoon Lemon Juice
  • 1 tablespoon Water
  • 1/8 teaspoon Cinnamon
  • 1/8 teaspoon Ground Ginger
  • 1 tablespoon Arrowroot Powder

For the Cookies

  • 1/3 cup Almond Flour Plus 2 tablespoons
  • 1/3 cup Tapioca Flour
  • 1/4 cup Coconut Flour
  • pinch of Kosher Salt
  • 1/4 cup Melted Coconut Oil
  • 2 tablespoons Unsweetened Applesauce
  • 1 tablespoon Pure Maple Syrup
  • 1/2 teaspoon Pure Vanilla Extract


  • Preheat oven to 350°F and line a baking sheet with parchment paper.
  • Combine all the ingredients for the blueberry filling except the arrowroot powder in a small sauce pan over high heat. Bring to a boil, stirring frequently to mash the blueberries.
  • Once boiling, reduce to medium-low and continue mashing blueberries as the sauce thickens and reduces for about 5-7 minutes.
  • Stir in the arrowroot powder, remove from heat and let cool to thicken.
  • Combine all the flour and salt in a medium bowl.
  • Whisk together the coconut oil, applesauce, maple syrup and vanilla in a small bowl.
  • Add the wet ingredients to the dry ingredients and stir until a wet dough forms.
  • Roll the dough into balls just smaller than golf ball size and place on the baking sheet.
  • Gently press down on the balls with your thumb to make and indent in the middle of the cookie for the filling. Use your fingers to press together any cracks around the sides of the cookies after doing this.
  • Bake for 12-14 minutes until the edges just start to turn light brown.
  • Remove cookies from the oven, let cool completely then spoon the blueberry filling into the indentation.

Nutrition Facts

Serving: 1SERVING | Calories: 149kcal | Carbohydrates: 15g | Protein: 2g | Fat: 10g | Saturated Fat: 5g | Polyunsaturated Fat: 0.1g | Monounsaturated Fat: 0.4g | Sodium: 7mg | Potassium: 37mg | Fiber: 3g | Sugar: 6g | Vitamin A: 17IU | Vitamin C: 3mg | Calcium: 24mg | Iron: 1mg

This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition information can vary for a variety of reasons. For the most precise nutritional data use your preferred nutrition calculator based on the actual ingredients you used in the recipe.

Cuisine American
Course Breakfast
Keyword blueberry thumbprint cookies, blueberry thumbprints, paleo blueberry thumbprints

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

Recipe Rating


Sunday 23rd of August 2020

This recipe is lovely! I didn't have any applesauce, and used an egg instead. It turned out absolutely perfect. The blueberry compote is delightful. Thank you for sharing this recipe!

Anne @fANNEtasticfood

Wednesday 5th of August 2015

Mental note: when stuck on a desert island, make sure Gina is with you and brings these cookies...

Making these ASAP!


Tuesday 4th of August 2015

We love finding new paleo sweets, and these must be pretty great if you would commit to eating only them for the rest of your life. Could we sub a different fruit for the filling, maybe strawberries or raspberries?

Running to the Kitchen

Wednesday 5th of August 2015

of course!

Jen @ sweetgreenkitchen

Tuesday 4th of August 2015

Looks so yummy!

Thalia @ butter and brioche

Monday 3rd of August 2015

All that gooey and sweet jammy center is making me drool! These look AMAZING.