
These gluten free thumbprint cookies are perfect for holiday gatherings or a sweet treat any time of year. Growing up, we always made a variation of these for Christmas morning and the jammy center never lasted long with my family around the table.
I first baked these after searching for something festive for my gluten free niece. They vanished from the cookie tray faster than any of the classic varieties.
Ingredients
- Pecans finely chopped: give every cookie a toasty crunch. Choose pecans that are fresh and unsalted for best flavor
- Almond flour: forms the soft cookie base and keeps everything gluten free. Look for finely ground flour for the best texture
- Coconut flour: adds delicate structure and the mildest hint of coconut. Choose finely milled coconut flour for a smooth dough
- Kosher salt: balances the sweetness. Use flaky kosher salt for even seasoning
- Baking powder: helps the cookies rise and hold their shape during baking. Make sure it is fresh for proper lift
- Coconut oil melted: lends moisture and richness without using dairy. Use unrefined for a light coconut aroma
- Maple syrup: sweetens naturally without processed sugar. Pure maple syrup brings a deep flavor
- Apple cider vinegar: helps activate the baking powder for a tender crumb. A little goes a long way
- Vanilla extract: gives warm bakery notes. Pure vanilla makes a noticeable difference
- Almond extract: brings an extra boost of marzipan flavor. Good quality almond extract really shines here
- Jam of your choice: provides the classic colorful center. Choose a thick fruit jam so it doesn't run or melt out
Step-by-Step Instructions
- Make the Dough:
- Mix the almond flour coconut flour salt and baking powder in a large bowl until fully combined and no lumps remain. Add the melted coconut oil maple syrup apple cider vinegar vanilla extract and almond extract. Stir thoroughly until a soft but cohesive dough forms and everything is evenly moistened
- Shape and Coat the Cookies:
- Scoop out small spoonfuls of dough and roll each one between your palms to create smooth balls about one inch wide. Place the chopped pecans into a shallow bowl and gently roll each ball to coat its surface with pecans pressing lightly so the nuts adhere
- Form the Thumbprints:
- Arrange the dough balls on a parchment lined baking sheet leaving a little space between each. Use your thumb to gently press an indent into the center of each cookie without flattening them completely. If you notice big cracks at the edges just pinch them together for a neat finish
- Fill with Jam:
- Using a small spoon drop a dollop of your chosen jam into the indentation of each cookie so that the center is filled but not overflowing
- Bake and Cool:
- Slide the baking sheet into a preheated 350 degree oven. Bake for twelve minutes until the edges are only just starting to brown and the cookies look dry and set. Remove from the oven but let them rest on the baking sheet for ten minutes before attempting to move. They will be soft at first but will firm up perfectly as they cool

Pecans are my secret favorite part as they give each creamy bite a gentle crunch. My daughter loves adding raspberry jam so every tray we bake is a color parade at our weekend brunches
Storage Tips
Store cookies in an airtight container at room temperature for up to four days. If stacking layer parchment between cookies to avoid sticking. For longer storage freeze in a single layer then transfer to a zip top bag for up to two months
Ingredient Substitutions
No pecans on hand Use chopped walnuts or pistachios. You can use honey in place of maple syrup for a different sweetness note. For a coconut free version use an equal amount of tapioca flour instead of coconut flour

Serving Suggestions
Serve with coffee or hot chocolate for an afternoon treat. These cookies make a cheerful addition to a holiday cookie platter or a thoughtful edible gift when wrapped in parchment and twine. Offer several jam flavors to create a vibrant dessert centerpiece
Cultural and Historical Context
Thumbprint cookies have roots in Swedish baking known as Hallongrotta meaning raspberry cave. Their signature jam center made these cookies a festive favorite at Scandinavian celebrations and they remain a charming nostalgic cookie classic worldwide
Frequently Asked Questions
- → Can I use a different nut instead of pecans?
Yes, you can substitute pecans with finely chopped walnuts or hazelnuts for a distinct flavor and similar texture.
- → What jam flavors work best for the center?
Raspberry, strawberry, apricot, or blackberry jams all pair beautifully, but you can use any favorite fruit spread.
- → How should I store these cookies?
Keep them in an airtight container at room temperature for up to 4 days, or refrigerate for a slightly longer shelf life.
- → Can I make these cookies ahead of time?
Absolutely. Prepare and bake in advance; the texture improves as they cool and set, making them perfect for make-ahead treats.
- → Is it possible to use another sweetener instead of maple syrup?
You may substitute honey or agave syrup, though this will slightly alter the flavor and texture.