Chocolate Thumbprint Shortbread Cookies

Posted by on Dec 2, 2013 in Christmas, Cookies, Desserts, Holiday | 2 comments

… A Classic Cookie for the Holidays!

Gluten-free Dairy-free Chocolate Thumbprint Shortbread Cookies

Chocolate Thumbprint Cookies are a classic Christmas cookie. Traditional in their characteristic puddle of creamy chocolate in the center, the foundation of the cookie has been made in countless variations such as peanut butter, oatmeal, sugar cookie, and basic vanilla refrigerator drop cookie dough, just to name a few.

One of my favorite variations is with a shortbread cookie base. I’ve tried creating gluten-free, dairy-free shortbread from many standard recipes. Most have a lovely flavor but simply don’t hold together well for a shaped cookie, such as a thumbprint, because shortbread typically doesn’t contain egg. My favorite shortbread cookie recipe, sans gluten and dairy, does contain one egg – and the texture is perfect every time. If you are vegan or need to be egg-free, certainly try using an egg substitute*.

The shortbread is tender, buttery, and melts in your mouth. This recipe is the same shortbread dough I use every year for my Chocolate Filled Pecan Sandies (aka Christmas Kiss Cookies). After trying so many different variations, I’ve decided that if it ain’t broke, don’t fix it. I’ve left out the nuts from the sandies for the thumbprints, but if you like them in the dough, feel free to put them back in. They don’t alter the integrity of the dough’s texture and the shortbread is delicious both ways.

Filled with a simple ganache, which is simply chocolate that stays slightly softer (in this recipe, at least) and has cream incorporated into it (no cream here), the center has a smooth and creamy texture when you bite into it. It is an excellent match for the tender cookie base and won’t cause the shortbread to crumble when you take a bite.

Gluten-free Dairy-free Chocolate Thumbprint Shortbread Cookies

As with the melt-in-your-mouth cookie, the ganache follows suit. The shortbread has a very mild flavor, not especially sweet, letting the ganache bring the sweetness without being overbearing. (You know what that means, right? I eat far more than I should.) To make these thumbprints even more festive for the holidays, try sprinkling crushed gluten- free, vegan candy canes or shredded coconut over the ganache center.

Make plenty of these little classic cookies since the recipe doubles and triples perfectly. They store for up to a week at room temperature, and freeze well. Big batches make for great gift giving, cookie exchanges, and party dessert platters. The dough can also be made in advance, wrapped in wax paper and stored in an airtight, re-sealable plastic bag in the fridge. Simply set out at room temp for 10-15 minutes before using.

Happy Holiday Baking!


Gluten-free Dairy-Free Chocolate Thumbprint Shortbread Cookies


No Shellfish BugNo Fish BugNo Peanut BugNo Soy BugNo Dairy BugNo Gluten BugPrep time: 10 minutes

Bake time: 18-20 minutes

Oven temp: 350ºF

Cool time: at least 10 minutes

Makes about 5 dozen (60) cookies



2 3/4 (330g) cups gluten-free all-purpose flour – I use Authentic Foods Bette’s Gourmet Four Flour Blend2

1/4 cup blanched almond flour – I use Honeyville

1/4 teaspoon guar gum

1/4 teaspoon salt

1/3 cup granulated sugar

8 ounces (1 cup or 2 sticks) margarine or softened butter – I use Earth Balance Natural Buttery Spread – red tub1

1 egg

1 teaspoon vanilla – McCormick’s is gluten free

6 ounces semisweet chocolate – I use Enjoy Life Semi-sweet Mini Chips

1 teaspoon organic coconut oil – room temp is fine



Preheat oven to 350ºF.  Line a baking sheet with parchment paper.

Combine all-purpose flour, almond flour, guar gum, and salt in a small mixing bowl. Stir well. Set aside.

Beat sugar and margarine in a stand mixer or with a hand mixer until sugar is dissolved. Scrape the bowl, then beat in egg and vanilla until well mixed. Add the flour mixture into the wet mixture, gradually and on low speed, until dough forms.

Scoop a ball of dough, using 30g of dough (equal to a level #60 scoop or about 1 level tablespoonful), then press a depression into center.

Place dough cookies on a prepared baking sheet, 20 per sheet, and bake on center oven rack at 350ºF for 18-20 minutes. The cookies don’t spread so dough thumbprints can be placed just 1 inch apart. The bottoms will become golden when the cookies are done, but the rest of the cookie will not color – that’s perfect!

Transfer baked cookies, still on parchment paper, onto cooling rack and let cool at least 10 minutes. They will completely crumble if you move them when they’re still warm.

Melt chocolate chips and coconut oil in a double boiler, or in a glass bowl set over a pot of simmering water. Remove chocolate from heat and let cool 5-10 minutes. It will thicken just slightly; that’s fine.

Ladle the melted chocolate using a teaspoon into the depression of each cookie, just until filled. Let rest at least five minutes, but the chocolate will take longer to set and become semi-solid. If you need to set the chocolate more quickly, slip the filled cookies still on the parchment paper back onto a cookie sheet, then place in freezer for 7-8 minutes. The thumbprint cookies will now be completely set and less delicate to handle. Store at room temperature, uncovered about an hour, or place in an airtight container. I have a metal cookie tin in which I love to store all of my cookies. Everyone at Daily Forage knows that if the tin is on the counter, there’s some sweet treat inside.

*To substitute one egg, use 1 Tablespoon flax meal or chia seeds combined with 3 Tablespoons hot water. Set aside for 10 minutes to become gelatinous. This will provide a perfect egg substitute in this recipe. Egg replacer may work (I’ve not tried it.) Substituting the egg with applesauce or fruit puree in this recipe will not work.

1Earth Balance Product Review

2Bette’s Gourmet Four Flour Blend Product Review 

Do you have great ways to use this versatile shortbread dough? Share with everyone in the comments below!

Safe food is a journey … Thrive!™

Other recipes you might enjoy:

Gluten-free Dairy-free Chewy Chocolate Espresso Gingerbread Cookies

Chewy Chocolate Espresso Gingerbread Cookies

Chocolate Filled Pecan Sandies

Chocolate Filled Pecan Sandies



  1. Thanks so much for this wonderful holiday recipe idea!

    • You’re quite welcome! Thanks for visiting Daily Forage. Be sure to subscribe to receive emails. There will be many more seasonal and holiday recipes coming very soon. I’d hate for you to miss any of them!

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