Peanut Butter Thumbprint Cookies with Jam

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These soft and chewy peanut butter thumbprint cookies are the perfect vessel for a dollop of strawberry jam! They’re a super fun little treat for all my fellow PB&J lovers and happen to be gluten free as well!

Peanut Butter Thumbprint cookies with a spoonful of raspberry jam

One of my favorite holiday traditions is mom and I’s annual cooking baking extravaganza. Each year, we set aside one full day in December to bake up a storm of Christmas cookies. We’ve made everything from Pecan Pie Bars to Strawberry Lemonade Linzer Cookies to Chocolate Dipped Fluffernutter Ritz Cookies. We like to switch things up, but one thing is always the same: we commit to an absurdly ambitious number of recipes and end the day in a puddle of exhaustion and frosting.

This past holiday season was more hectic than usual (chalk that one up to the arrival of a certain someone), so mom and I decided to put off our traditional bake-till-you-drop day off until January. After all, why should the holidays get all the cookies? Goodness knows these cold and dreary January days could use some sweet treats.

Peanut Butter Thumbprint Cookies on a sheet pan

Mom and I finally got together last week, and while our attempt at gingerbread houses was a massive (albeit hilarious) fail, these Peanut Butter Thumbprint Cookies were a raving success. They’re soft and chewy, easy to make, great for baking with kids, and taste just like a sweet, bite size PB&J. What’s not to love?

These cookies also happen to be gluten free. Mom can’t tolerate gluten, so we make almost all of our cookies gluten free these days. Luckily, these were still a cinch to make and the dough is so soft, tender, and delicious, no one would guess they’re gluten free! Still, if you prefer (or if it’s what you have on hand), feel free to sub all purpose flour for the gluten free flour. 

Peanut butter thumbprint cookies with a hand grabbing a cookie

How do you make a thumbprint cookie?

Not surprisingly, thumbprint cookies are made by pressing your thumb into the center of a ball of cookie dough to create a perfect little canyon for a variety of fillings. If you prefer not to use your fingers to make a thumbprint, you can also use the rounded handle end of a wooden spoon. If you’re making these with kids, they’ll love using their thumbs to create the prints in the center!

This version of thumbprint cookies is made with a super simple gluten free peanut butter dough you can whip up in 20 minutes or less. I love the combination of peanut butter and jam, but feel free to experiment with other fillings, like chocolate ganache or nutella. You can also use this dough to make gluten free peanut butter blossoms, like these!

If the thumbprint dips raise too much during baking, you can press your thumb into them gently again after baking to ensure you have a good sized hole in the center for filling.

There are a couple different schools of thought regarding whether you add the jam before or after baking these. We experimented with both methods and found we liked filling them after baking better. This allowed the cookies to bake more evenly, and helped them keep for longer as well. (More on that below!). We also loved using different kinds of jam based on our mood– strawberry, raspberry, blackberry, or grape are all great options for classic PB&J cookies.

peanut butter thumbprint cookies filled with berry jam

Do you have to refrigerate thumbprint cookies?

I recommend refrigerating these Peanut Butter Thumbprint Cookies for an hour before baking so they keep their shape.

How long will thumbprint cookies keep?

If you wait to fill these until after baking, they’ll keep for up to a week in an airtight container. You can fill just a few at a time to enjoy whenever a craving hits!

peanut butter thumbprint cookies filled with strawberry jam

Can thumbprint cookies be frozen?

You can absolutely freeze these Peanut Butter Thumbprint Cookies. I recommend freezing them after baking, but before filling them. Remove from the freezer and thaw at room temperature before filling.

For more tips on freezing cookies and saving them for later, check out our Ultimate Guide to Freezing Cookies and Bars.

If you’re feeling a post-holiday baking itch, or your January just needs a little cheering up, I highly recommend whipping up a batch of these Peanut Butter Thumbprint Cookies! They’re the perfect little pick me up for any time of year, and short of making a full blown Grilled PB&J sandwich, these allow you to indulge your craving, but in a more bite-sized form factor.

peanut butter thumbprint cookies with a bite taken out
peanut butter thumbprint cookies filled with berry jam

Peanut Butter Thumbprint Cookies with Jam

Soft, tender gluten free peanut butter cookie with a dollop of jam in the center.
5 from 3 votes
Print Pin
Prep Time: 15 minutes
Cook Time: 10 minutes
Rest Time: 1 hour
Total Time: 1 hour 25 minutes
Servings: 48
Calories: 101kcal


  • 1 1/4 cups brown sugar
  • 1 cup creamy peanut butter
  • 1/2 cup butter
  • 2 large eggs
  • 1/2 teaspoon vanilla extract
  • 2 cups All-Purpose Gluten Free Flour (*see note)
  • 1/2 teaspoon Xanthan Gum (*see note)
  • 1 teaspoon baking soda
  • 1/2 teaspoon Kosher salt
  • 1/2 cup jam


  • Combine the butter, peanut butter and brown sugar in the bowl of a stand mixer. Beat on medium speed until light and fluffy. Add the eggs, one at a time, beating well after each addition. Beat in the vanilla extract.
  • In another bowl, whisk together the gluten-free flour, xanthan gum, baking soda and salt. Add this mixture to the peanut butter mixture and beat until just combined. Transfer the dough to a piece of plastic wrap and cover it. Refrigerate for at least one hour or overnight.
  • Pre-heat oven to 375°F. and Line a baking sheet (or several, if you have them!) with parchment paper. Use a medium cookie scoop to scoop tablespoons of dough onto the cookie sheet. Use a thumb or the handle end of a wooden spoon to make a divot in the center of each cookie. Bake for 7-9 minutes or until puffed and mostly set.
  • If the divots rise too much during baking, just use your thumb to press them back down as they cool.
  • Allow the cookies to cool completely, then fill each divot with about a 1/2 teaspoon of jam. Depending on the thickness of your jam, you may want to microwave it for ten seconds to make filling easier.


  • We used Bob’s Red Mill All Purpose Gluten Free Flour. If you don’t need these to be gluten free, you can substitute all purpose flour for the gluten free flour and omit the xanthan gum.
  • We like to store these unfilled in an airtight container for up to a week. The unfilled cookies can also be frozen. Once filled, they will keep for about 2 days.
Course Cookies
Cuisine American
Keyword gluten free cookies, gluten free thumbprints, peanut butter and jelly, peanut butter and jelly cookies, peanut butter cookies, peanut butter thumbprints, thumbprint cookies


Serving: 1cookie | Calories: 101kcal | Carbohydrates: 13g | Protein: 2g | Fat: 5g | Saturated Fat: 2g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.1g | Cholesterol: 13mg | Sodium: 92mg | Potassium: 44mg | Fiber: 1g | Sugar: 8g | Vitamin A: 70IU | Vitamin C: 0.3mg | Calcium: 13mg | Iron: 0.4mg
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Peanut Butter Thumbprint Cookies with jam in the center

5 from 3 votes (3 ratings without comment)

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