Plain Gluten Free Thumbprint Cookies with Chocolate Filling

Plain Gluten Free Thumbprint Cookies with Chocolate Filling

A tray of thumbprint cookies with chocolate on top
I have thumbprint recipes all over the place, to be honest (my first book, my second book, even a chocolate one on this blog), but I was still antsy about the thumbprints. I wanted a solution to the disappearing thumbprint once and for all—one that allowed us to fill the print after baking. You can imagine the failed buttery cookies my family has eaten over the last couple weeks.

A close up of thumbprint cookies with chocolate on top on a metal tray

Up until now, my best solution was to bake the cookies for 5 minutes, press a thumb (or more likely a 1/2 teaspoon), fill, and then finish baking. Not bad, but what if you don’t want to bake the filling, like, at all?! Well well well. Well.

Thumbprint cookies on brown surface being filled with chocolate

And that’s it. I rejiggered the recipe so that it’s a bit lighter and fluffier, which helped the print stay in place. And then I even used some insurance in the form of … pie weights.

But the pie weights really aren’t that necessary. The balance of ingredients in this recipe really takes care of the problem on its own. But still, I’m a big believer in insurance. I always consider it money well-spent, and if I don’t ever cash in? Good for me.

Overhead view of thumbprint cookies with chocolate on top on a brown surface

You are hereby free to fill these thumbprint cookies with whatever you like. I filled it with a very stable mostly-chocolate mixture, but you could totally fill it with a chocolate ganache.

Or even candy! How cute would that be?! Maybe even some marshmallow fluff? That stuff makes me weak in the knees. How about Jello, for something of a stained glass effect? Go for it!! Cookie Season, we’re ready for you!

Like this recipe?

Prep time: Cook time: Yield: 12 cookies


1 cup (140 g) all purpose gluten free flour (I used my Better Than Cup4Cup blend, but any of the blends in the link would likely work fine)

1/2 teaspoon xanthan gum (omit if your blend already contains it)

4 tablespoons (36 g) cornstarch (if you can’t have cornstarch, maybe try arrowroot?)

1/4 teaspoon kosher salt

3/4 cup (86 g) confectioners’ sugar

8 tablespoons (112 g) unsalted butter, at room temperature

1 egg (60 g, out of shell) at room temperature, beaten

1 teaspoon pure vanilla extract

5 ounces semi-sweet chocolate, chopped (chips would work fine, too)

3 tablespoons (36 g) vegetable shortening (I use Spectrum nonhydrogenated vegetable shortening)


  • Preheat your oven to 325°F. Line a rimmed baking sheet with unbleached parchment paper and set it aside.

  • In a large bowl, place the all purpose flour blend, xanthan gum, cornstarch, salt and confectioners’ sugar, and whisk to combine well. Create a well in the center of the dry ingredients, and add the butter, egg and vanilla, mixing to combine after each addition. The dough will be thick but soft. Divide the dough into 12 equal pieces. Roll each into a ball, and then flatten into a disk about 1/2 inch thick. Press the moistened bowl of a 1/2 teaspoon (or your thumb, moistened) into the center of each disk, about 3/4 of the way to the bottom of the dough. If the dough begins to stick to the teaspoon or your thumb, moisten it in between each cookie. To ensure that your divot remains after baking, you can place a small piece of unbleached parchment paper in each divot, and top with a couple dried beans or pie weights.

  • Place the cookies in the center of the preheated oven and bake for 10 minutes, or until the cookies are puffed and set. They will only brown a bit around the edges. Remove the cookies from the oven, allow to cool for about 5 minutes on the baking sheet, and then remove the weights and parchment paper (if you used them). Transfer to a wire rack to cool completely.

  • While the cookies are cooling, make the chocolate filling. Place the chopped chocolate (or chips) and the shortening in a small, heat-safe bowl. Place over a small pot of simmering water, taking care to ensure that the bowl does not touch the water. Heat, stirring occasionally, until the mixture is melted and smooth. Remove from the heat and allow to cool for about 5 minutes or until it just begins to thicken. Pour into the wells of the cooled cookies and allow to sit at room temperature until set (about 45 minutes). If you’re in a hurry, place the cookies in the refrigerator to speed things up a bit.



P.S. Thank you so much for all your support of the new book, GFOAS Bakes Bread! Last night’s Live Facebook Q&A was awesome. You were out in full force! I hope it helped ease your concerns about baking yeast bread. And we’ll totally do it again, maybe next week if you’re into it!

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