Buttery chocolate cookies coated with sugar and filled with a luscious chocolate ganache make up these incredible Chocolate Thumbprint Cookies. If that wasn’t enough, they’re gluten free, egg free, nut free and can easily be dairy free (vegan)!
The chocolate obsession in this house is real. My daughter, my son and I are all addicted. We can’t get enough.
This chocolate thumbprint cookie recipe is one of our absolute favorite dessert recipes. They look like they’re a lot of work but they really aren’t that involved.
I love how they’re bite size…it makes me feel slightly better about eating so many of them!
For more thumbprint cookie, try my Lemon Thumbprint Cookies and Raspberry Lemonade Cookies.
Tips for making the Cookie Dough
Mix the dry ingredients- In a large bowl, using a whisk, mix together the gluten free flour, cocoa powders and salt. Set aside.
Cream the sugar and butter or vegan baking stick- In a large bowl of an electric mixer fitted with a paddle attachment, or using a hand mixer, beat the softened butter or vegan baking stick with one cup of the granulated sugar until soft and fluffy. About 2-3 minutes.
Make the cornstarch water mixture- In a small bowl, using a spoon, mix together the cornstarch and water until it is thin and watery. It will be thick and tacky at first.
Add the gf flour mixture and milk of choice- Starting and ending with the gluten free flour mixture, alternate between pouring the gluten free flour mixture and milk of choice into the bowl of the electric mixer until just combined. The dough will be very thick, you might need to work it with your hands a bit.
Freeze the dough- Remove dough from bowl, form a disc shape, wrap in plastic wrap and freeze for 30 min. You could put it in the fridge but then I would chill it for at least an hour.
Let’s Roll
Make 1 inch dough balls- Break one inch pieces off the dough and roll into balls.
Coat the dough balls in sugar- Drop the balls into granulated sugar to coat and place two inches apart on the baking sheet.
Create the well- Push your thumb or pointer finger into the center of each ball to create a well. Reshape the cookie to make sure it is round, if needed.
Bake the cookies- Bake for 11 min. Remove from the oven and let cool on the baking sheet for a few min. If the holes need to be fixed, gently press the bottom of a wooden spoon into the holes to fix. Don’t use your thumb or you’ll burn your finger! Speaking from experience here.
Let them cool- Leave them on the baking sheet for about 2 minutes then move them to the cooling rack and make the filling.
Make the Ganache
In a microwave safe bowl, combine all the filling ingredients- Microwave in 15 second increments, stirring after each time, until completely melted.
Pour in the ganache- Use a tiny spoon to pour the filling into each hole of each cookie.
You can serve them right away when they’re all gooey or wait till they’re cool when the filling solidifies. Either way they’re delicious!
Can these cookies be vegan?
Yes! Here are some tips to make them vegan:
- Use a gluten free flour that’s free from dairy.
- Swap the butter for vegan baking stick
- Make sure to use a non dairy milk of choice.
- Only use dairy free/allergy friendly chocolate chips like ones from Enjoy Life.
Cookie Time
Now it’s time to bite into these decadent gluten free/allergy friendly chocolate thumbprint cookies! I love to eat them all the time obviously BUT they are unbelievable when the ganache is still gooey! Finger licking good! Hope you love them as much as we do!! Enjoy!
Other Chocolate Cookies To Try

Chocolate Thumbprint Cookies
Ingredients
For the cookies:
- 2 ⅔ cups gluten free flour
- ⅓ cup cocoa powder I fill half the ⅓ cup with Dutch cocoa and half of the ⅓ cup with dark cocoa powder
- ½ teaspoon kosher salt
- 1 cup granulated sugar plus ¼ cup for rolling
- 2 sticks unsalted butter or vegan baking stick softened
- 2 heaping tablespoons cornstarch mixed with 3 tablespoons water
- ⅓ cup milk of choice
- 2 teaspoons pure vanilla extract
For the filling:
- ¾ cup semi sweet chocolate chips use dairy free and nut free for vegan/allergy friendly
- 1.5 teaspoons light corn syrup
- 4 tablespoons unsalted butter or vegan baking stick
Instructions
- In a large bowl, using a whisk, mix together the gluten free flour, cocoa powders and salt. Set aside.
- In a large bowl of an electric mixer fitted with a paddle attachment, or using a hand mixer, beat the softened butter or vegan baking stick with one cup of the granulated sugar until soft and fluffy. About 2-3 minutes.
- In a small bowl, using a spoon, mix together the cornstarch and water until it is thin and watery. It will be thick and tacky at first.
- Beat the cornstarch water mixture and vanilla into the butter and sugar until combined.
- Starting and ending with the gluten free flour mixture, alternate between pouring the gluten free flour mixture and milk of choice into the bowl of the electric mixer until just combined. The dough will be very thick, you might need to work it with your hands a bit.
- Remove dough from bowl, form a disc shape, wrap in plastic wrap and freeze for 30 min.
- Preheat your oven to 325 degrees Fahrenheit. Line your baking sheet with parchment paper.
- Break one inch pieces off the dough and roll into balls. Drop the balls into granulated sugar to coat and place two inches apart on the baking sheet. Push your thumb or pointer finger into the center of each ball to create a well. Reshape the cookie to make sure it is round, if needed.
- Bake for 11 min. Remove from the oven and let cool on the baking sheet for a few min. If the holes need to be fixed, gently press the bottom of a wooden spoon into the holes to fix. Don’t use your thumb or you’ll burn your finger! Speaking from experience here.
- Move the cookies to a cooling rack and make the filling.
- In a microwave safe bowl, combine all the filling ingredients. Microwave in 15 second increments, stirring after each time, until completely melted. Use a tiny spoon to pour the filling into each hole of each cookie. You can serve them right away when they’re all gooey or wait till they’re cool when the filling solidifies. Either way they’re delicious! Enjoy!
- Notes: Feel free to use natural unsweetened cocoa powder instead of Dutch. Also, if you only want to use one type of cocoa powder, use Dutch or natural unsweetened and NOT all dark. If you use all dark the cookies will be dry. Keep in mind if you don’t add the dark cocoa powder, your cookies will be much lighter in color than mine.
Nutrition
This recipe for Double Chocolate Thumbprint Cookies was adapted from Martha Stewart's Chocolate Cookie Dough and Martha Stewart's Thumbprint and Ball Cookies.
john
This is my absolute favorite cookie!