Gluten-Free Maple Pecan Pie Thumbprint Cookies

These gluten-free Maple Pecan Pie Thumbprint Cookies combine a tender, buttery cookie with a rich maple pecan filling with little pockets of semi-sweet chocolate. The cookie is delicate and lightly sweet, while the filling brings the deeper flavors of pecans, pure maple syrup, butter, and chocolate.

The result is a cookie with a soft, tender texture and a filling that is slightly gooey when warm and firms as it cools.

They have all the buttery and tender flavors of pecan pie tucked into a bite-sized cookie, making them especially lovely for holiday cookie trays, dessert platters, or simply enjoying with a cup of coffee.

You may also enjoy my classic Gluten-Free Thumbprint Cookies, or my delicious Gluten Free Linzer Cookies.

RECIPE HIGHLIGHTS

• Gluten-free: Made with a gluten-free 1:1 measure-for-measure flour blend.
• Tender and buttery: Powdered sugar gives the cookie a delicate texture.
• Maple pecan filling: Pure maple syrup provides the sweetness without brown sugar.
• Chocolate pockets: Semi-sweet chocolate chips are stirred into the warm filling so they don’t completely melt.
• Easy to shape: A large cookie scoop keeps the cookies consistent, while a small melon-sized scoop makes portioning the filling simple.
• Make-ahead friendly: The shaped and filled cookies can be chilled in the freezer just before baking. Allow extra time for baking.

Or try my favorite Gluten Free Chocolate Pecan Pie.

KEY INGREDIENTS AND SWAPS

Gluten-free 1:1 flour blend

I used King Arthur Gluten-Free Measure for Measure Flour, which weighs approximately 120 g per cup. The recipe uses 2½ cups (300 g) of this flour.

Important: Gluten-free flour blends do not all weigh the same per cup. If you use a different gluten-free 1:1 flour blend, weigh the flour rather than assuming 300 g will equal 2½ cups of your particular blend. The amount of flour can significantly affect the texture and shape of these cookies.

Powdered sugar

Powdered sugar helps create the tender, delicate texture of these thumbprint cookies. Check the label to make sure your powdered sugar is gluten-free.

Pecans

Finely chopped pecans work best for the filling because they fit neatly into the thumbprints and distribute throughout the maple mixture.

Pure maple syrup

Use pure maple syrup, rather than pancake syrup or maple-flavored syrup. It is gluten-free and gives the filling its characteristic maple flavor and pairs beautifully with the pecans.

Semi-sweet chocolate chips

I use gluten-free semi-sweet chocolate chips. Mini chocolate chips work especially well because they distribute easily throughout the filling without overpowering the pecans.

TIPS AND FAQS

Why do I need to weigh the gluten-free flour?

This is one of the most important details in gluten-free recipes. Gluten-free flour blends can have significantly different weights per cup depending on the ingredients and proportions in the blend.

I developed this recipe using King Arthur Gluten-Free Measure for Measure Flour, which weighs approximately 120 g per cup. For this reason, I provide both the cup measurement and 300 g for that specific blend.

If you use another gluten-free flour blend, don’t assume that 2½ cups will also weigh 300 g. 

Can I use a different gluten-free flour blend?

Yes, but choose a 1:1 measure-for-measure gluten-free baking blend intended to replace all-purpose flour. Because blends vary, weighing the flour is especially important.

Why freeze the cookies before baking?

After filling the thumbprints, the cookies are placed in the freezer for 10 minutes. This helps firm the butter and filling before the cookies go into the oven, helping them maintain their shape.

Can I use a different type of chocolate?

Semi-sweet chocolate provides a nice contrast to the maple and pecans without making the filling overly sweet. You could use dark chocolate for a more bittersweet flavor.

How do I portion the cookies?

I use a large cookie scoop for the dough and a small melon-sized scoop for the pecan filling. This makes it easy to create evenly sized cookies without weighing individual portions.

Should the chocolate chips melt completely?

It depends. If you want pockets of chocolate, after cooking the maple pecan mixture, let it cool for about 10 minutes before adding the chocolate chips. Give them just a quick stir. They don’t need to fully melt. This leaves little pockets of chocolate throughout the filling.

Or, add them when the mixture is still hot for chocolate pecan texture.

WHAT TO SERVE WITH MAPLE PECAN THUMBPRINT COOKIES

These cookies are wonderful on their own, but they can easily become part of a more decadent dessert.

• Chocolate drizzle: Drizzle the cooled cookies with melted chocolate or gluten-free chocolate sauce for an extra chocolate finish.
• Vanilla ice cream: Serve a warm cookie alongside a scoop of vanilla ice cream for a simple maple pecan pie-inspired dessert.
• Dessert platter: Arrange them with other gluten-free cookies, bars, and small desserts for an elegant gluten-free dessert spread.
• Coffee or tea: Their buttery pecan and maple flavors pair particularly well with coffee, or chai.

Storing To Keep The Gluten-Free Maple Pecan Pie Thumbprint Cookies

Store cooled cookies in an airtight container at room temperature for up to 3 days.

For longer storage, refrigerate them in an airtight container for up to 1 week. Bring them to room temperature before serving for the best texture.

The cookies can also be frozen in an airtight freezer-safe container. Place parchment between layers to prevent sticking.

Hi, I’m Kristina, a gluten-free recipe developer creating and testing recipes since 2012. Every recipe on this site is made in my kitchen and personally tested (with the help of my very honest family!).

Did you make this recipe? I’d love to hear how it turned out! Leave a ⭐⭐⭐⭐⭐ rating and a quick review below, it helps other gluten-free cooks discover recipes they can trust.

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