Gluten-Free Chocolate Pecan Thumbprint Cookies

Gluten-Free Chocolate Pecan Thumbprint Cookies
Gluten-Free Chocolate Pecan Thumbprint Cookies

Happy holidays! Hoping everyone is having a beautiful day, where ever you are and whatever you are up to. We’re taking it easy, with no fancy plans, aside from maybe making a fresh batch of eggnog. I am so thankful to have a break from the hustle and bustle of the rest of the year — time to slow down, get outside (fingers crossed for some warmer weather later this week! 🤞), and even some creative recipe development without the time constraints of the normal work week (been working on lots of videos! Check out this one for homemade loose leaf chai! Also still trying to use up all of the spaghetti squash harvest from the garden). And, eating these gluten-free chocolate pecan thumbprint cookies!

These cookies.

Just almond flour, honey, butter, salt and baking soda combine to make a surprisingly soft but sturdy and satisfying cookie, something I discovered when I made these Paleo chocolate vanilla pinwheel cookies two years ago (2016 seems like so long ago! We had just moved into our house, I remember rolling out the cookie dough next to the wall between our kitchen and dining table. Just a few weeks later, we removed the wall and the house looks about 1,000x better! But I digress...)

Thumbprint cookies — a Swedish treat traditionally made with a raspberry filling - have always looked festive to me. When filled with raspberry jam, they gleam in the light like little gems. But raspberry is a very summery flavor, and my inner chocoholic screamed “ganache!!” and I gave in easily, filling each with a melted 85% Dark Chocolate Lindt Bar.

Gluten-Free Chocolate Pecan Thumbprint Cookies
Gluten-Free Chocolate Pecan Thumbprint Cookies

The result is similar to those chocolate kiss-topped peanut butter cookies we’ve all had at many a Christmas party, but with more delicate flavors. Toasted pecans with chocolate is an unparalleled combo in desserts in my book, one that fills your kitchen with the smells of caramelly nuts and fruity cacao scent.

The cookie dough in this recipe is fairly flexible when it comes to flour. I tested using 1/2 cup gluten-free measure for measure flour (King Arthur flour) in place of 1/2 cup of almond flour and the result was almost the same as using all almond flour. That’s not to say I’ve tested everything! But I’m confident you’ll love these. The dough will crack a bit when you go to make the thumbprints, but that doesn’t impact the cookie much. We’re not going for perfect here — once you add the chocolate and the pecans, they’ll look (and be) absolutely delicious!

Gluten-Free Chocolate Pecan Thumbprint Cookies
Gluten-Free Chocolate Pecan Thumbprint Cookies

Gluten-Free Chocolate Pecan Thumbprint Cookies

Published December 25, 2018 by
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Yield: 15   |    Active Time: 40 minutes


  • 2 cups almond flour
  • 1/4 teaspoon salt
  • 1/4 teaspoon baking soda
  • 1/4 cup coconut oil or butter, melted
  • 1/4 cup honey
  • 1/2 teaspoon vanilla extract

  • For the filling:
  • 1/3 cup chocolate chips (or a chopped up dark chocolate bar)
  • 1 tablespoon coconut oil or butter
  • 1/2 cup pecan halves, toasted

  • Directions:

    1. Preheat oven to 325°F. Line a cookie sheet with parchment paper and set aside.
    2. In a medium-sized mixing bowl, combine almond flour, salt, and baking soda and whisk briefly to combine.
    3. Add melted oil/butter, honey, and vanilla and stir dough with a spatula until a stiff dough forms.
    4. Shape cookies: scoop cookie dough by the tablespoonful into the palm of your hand. Shape into a sphere, and then place on a prepared cookie sheet. Using a smaller spoon or you thumb, make an indent in the center of the cookie. The dough may crack a bit around the edges, which is fine; if you like, you can carefully press it together with your fingers.
    5. Repeat step 4 until all of the dough is used. Leave at least 1/2 inch between each cookie on the baking sheet.
    6. Place cookies in oven on middle rack and bake for 10-13 minutes. Cookies should be golden and fragrant. Set aside to cool.
    7. While cookies cool, make the filling. Melt chocolate and 1 tablespoon butter/oil in a microwave safe bowl in the microwave by heating at 30-second intervals, stirring between each round, or in a double boiler.
    8. When cookies have cooled enough to be easily handled, carefully spoon chocolate into the center of each, and place a single pecan half in the center of each. Allow chocolate to set for 10-15 minutes, and then serve or store in an air-tight contain for a week.