These Chocolate Thumbprint Cookies are buttery chocolate cookies coated with sugar and filled with a luscious chocolate ganache. They're decadent yet sweet and the most perfect treat! If that wasn’t enough, they’re gluten free, egg free, nut free and can easily be dairy free (vegan)!
These chocolate thumbprint cookies are one of our absolute favorite dessert recipes. They look like they’re a lot of work but they really aren’t that involved and only take about an hour from start to finish.
I love how they’re smaller…it makes me feel slightly better about eating so many of them like with my Mini Chocolate Chip Cookies!
If you're looking for more thumbprint cookie recipes, try my Chocolate Blossom Cookies, Lemon Thumbprint Cookies and Raspberry Lemonade Cookies.
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Reasons to Love these Cookies
- Allergy Friendly- These cookies are gluten free, nut free, egg free and can easily be dairy free (vegan)!
- Soft & Chewy Inside- The cookies are thick, soft and chewy!
- Ganache Center- They have a chocolate ganache center that oozes when warmed!
- Double Chocolate- There is chocolate in two different ways like in our Chocolate Blossom Cookies!
Ingredient Notes
- Gluten Free Flour- If you also have nut allergies, make sure to use a brand that’s made in a nut free facility. I really love to use this gluten free flour because it’s nut safe but it does contain dairy. It also contains xanthan gum which really helps give baked goods their bounce.
- Vegan Baking Stick/Butter- Only use room temperature. If you use melted, the cookies will spread too much while baking.
- Cornstarch and Water- These are eggless cookies so this mixture helps bind everything together.
- Milk- If there are no dairy allergies or if you’re not vegan, you can use regular whole milk. For non dairy, use a non dairy milk of your choosing.
- Chocolate Chips- Make sure to use allergy friendly to make these vegan.
- Corn Syrup- This gives the filling that gorgeous shine. You can leave it out but keep in mind the chocolate will be more matte.
See my recipe card below for a complete list of the ingredients with measurements.
Substitutions and Variations
How to Make these Vegan
- Use a gluten free flour that’s free from dairy.
- Make sure the brand of sugar you use is vegan.
- Use vegan baking sticks instead of butter.
- Only use a non dairy milk of choice.
- Read the label on your chocolate chips to ensure they’re gluten free, nut free and vegan.
How to Make this recipe with All Purpose Flour
- Use 2 ⅔ packed cups of regular flour (448 grams).
- Make sure to also use packed cups of cocoa powder.
- Use 2 tablespoons of milk.
- You still need to chill the dough due to the lack of eggs.
This recipe has not been tested with these substitutions and/or variations due to celiac disease and food allergies. If you change any of the ingredients, please let us know how the recipe turned out in the comments below!
How to Make Chocolate Thumbprint Cookies
Here are the step by step instructions to make these cookies!
Make the Cookies
Step 1: Whisk Together the Dry Ingredients
In a large bowl, combine the gluten free flour, both cocoa powders and salt. Whisk to combine.
Step 2: Make the Cornstarch Water
In a small bowl, using a spoon, mix together the cornstarch and water until thin and watery. It will be thick and tacky at first.
Step 3: Cream the Sugar
In a large bowl of an electric mixer fitted with the paddle attachment or using a hand held mixer, beat the room temperature butter or vegan butter and 1 cup of sugar until soft and creamy. About 2 minutes.
Step 4: Add in the Cornstarch Water and Vanilla
Slowly beat in the cornstarch water mixture and the vanilla. It's ok if it looks chunky.
Step 5: Add the GF Flour Mixture and Milk
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.
Step 6: Freeze the Dough and Preheat the Oven
Remove dough from bowl, shape into a round flat disc, wrap in plastic wrap and freeze for 30 minutes or chill in the fridge for at least 1 hour. It needs to harden otherwise the cookies will spread all over the place. You can even chill overnight.
When the dough is almost done chilling, preheat the oven to 325 degrees Fahrenheit and line a baking sheet with parchment paper.
Step 7: Scoop the Dough and Drop in Sugar
Remove dough from the freezer or fridge and use a small cookie scoop or use your hands to roll dough into 1 inch balls.
Pour the ½ cup of granulated sugar into a bowl. Drop each dough ball into the sugar and coat completely.
Step 8: Make the Well and Bake the Cookies
Place the cookies on the baking sheet about 2-3 inches apart. 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.
Pop the extra dough balls into the fridge while these are baking. Bake the cookies in the center rack of the oven at 325 degrees Fahrenheit for 11 minutes.
Immediately reshape the cookies when they come out of the oven and 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 the cookies cool on the baking sheet for 5 min before transferring to a cooling rack. If you don't do this, the cookies will break apart into a giant mess.
Make the Ganache
Step 1: Melt the Chocolate
Place the chocolate chips, butter and corn syrup in a microwave safe bowl. Heat in 15 second increments, stirring after each time, until completely melted and incorporated.
Step 2: Fill the Cookies
Use a tiny spoon to pour the chocolate ganache 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!
Expert Baking Tips
- Use 2 Types of Cocoa Powder- The 2 types of cocoa powders give the cookies their dark hue. If you only have one type on hand, use natural unsweetened or dutch...just know their color will not be as dark as mine. DO NOT use dark alone; it will make your cookies too dry and bitter.
- Use Room Temperature Butter- Do NOT use softened or melted butter/vegan baking sticks. The cookies will spread out when baking into a giant mess.
- Chill the Dough- If you don’t chill the dough for at least an hour, the cookies will spread and be flat and thin.
- Melt the Chocolate Slowly- If you rush this process and try to even heat the chocolate in 20 second increments (instead of 15 second increments), you can overheat the chocolate. If that happens it will seize up and basically not be usable.
- Reshape the Cookies- If you want your cookies nice and round, reshape them as soon as they come out of the oven. Either use a spatula to push them back into a circle shape or use a large circle cookie cutter. If using a cookie cutter, place it over the cookies and rotate quickly in a circle. Then use a wooden spoon end to reshape the cookie well if needed, while the cookies are right out of the oven.
Recipe FAQs
You can make the dough the night before. Shape into a disc, wrap in plastic and keep in the fridge.
If doing this, there is no need to chill again prior to baking.
Or you can wrap the dough in plastic and freeze the dough for up to 30 days. Thaw the dough in the fridge the night prior to using.
Most gluten free baked goods are best made the same day, but you can make these cookies a day before and store them in an airtight container at room temperature.
Once the ganache has hardened a bit, store cookies in an airtight container at room temperature for up to 3 days.
If you want them warm and gooey, heat the cookie in the microwave for a few seconds prior to serving. Be careful not to burn your mouth on the hot ganache.
Other Chocolate Cookie Recipes You'll Love
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📖 Recipe
Chocolate Thumbprint Cookies
Ingredients
For the Cookies:
- 2 ⅔ cups gluten free flour (I use a 1:1 gf flour with xanthan gum)
- 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 ½ cups granulated sugar , reserve ½ cup for rolling
- 1 cup unsalted butter or vegan baking stick, room temperature
- 2 heaping tablespoons cornstarch mixed with 3 tablespoons water
- ⅓ cup milk
- 2 teaspoons pure vanilla extract
For the Ganache:
- ¾ cup semi sweet chocolate chips
- 4 tablespoons unsalted butter or vegan baking stick
- 1 ½ teaspoons light corn syrup
Instructions
- In a large bowl, using a whisk, mix together the gluten free flour, cocoa powders and salt. Set aside.
- 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.
- In a large bowl of an electric mixer fitted with a paddle attachment, or using a hand mixer, beat the butter or vegan baking stick with one cup of the granulated sugar until soft and fluffy. About 2-3 minutes.
- 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, shape into a round flat disc, wrap in plastic wrap and freeze for 30 minutes or chill in the fridge for at least 1 hour. It needs to harden otherwise the cookies will spread all over the place. You can even chill overnight. When the dough is almost done chilling, preheat the oven to 325 degrees Fahrenheit and line a baking sheet with parchment paper.
- Remove dough from the freezer or fridge and use a small cookie scoop or use your hands to roll dough into 1 inch balls.Pour the ½ cup of granulated sugar into a bowl. Drop each dough ball into the sugar and coat completely.
- Place the cookies on the baking sheet about 2-3 inches apart. 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.
- Pop the extra dough balls into the fridge while the first group are baking. Bake the cookies in the center rack of the oven at 325 degrees Fahrenheit for 11 minutes.
- Immediately reshape the cookies when they come out of the oven and 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 the cookies cool on the baking sheet for 5 min before transferring to a cooling rack. If you don't do this, the cookies will break apart into a giant mess.
Make the Ganache
- Place the chocolate chips, butter and corn syrup in a microwave safe bowl. Heat in 15 second increments, stirring after each time, until completely melted and incorporated.
- Use a tiny spoon to pour the chocolate ganache 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!
john
This is my absolute favorite cookie!