These Chocolate Thumbprint Cookies are buttery shortbread 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 my family's 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.
This recipe makes 40 small cookies; perfect for bakes sales, holiday cookie swaps or holiday gatherings! 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!
For more thumbprint cookie recipes, try my Chocolate Blossom Cookies, Lemon Thumbprint Cookies and Raspberry Lemonade Cookies.
Reasons to Love these Chocolate Thumbprint Cookies
- Allergy Friendly- These cookies are gluten free, nut free, egg free and can easily be dairy free (vegan)!
- Crumbly Texture- The insides of these cookies are crumbly yet buttery and soft! They melt in your mouth!
- Covered in Granulated Sugar- The sugar coating gives the outside a nice crunch!
- 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 free of the top 9 allergens. It also contains xanthan gum which really helps give baked goods their bounce and prevents them from falling apart.
- Cocoa Powders- I like to use two types to give the cookies a dark color (like in my Cinnamon Chocolate Cookies), but if you only want to use one, use Dutch or Natural Unsweetened. Do not only use Dark.
- 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 dairy-free milk of your choosing.
- Chocolate Chips- To keep allergy safe, make sure to use gluten free/vegan chocolate chips. I love these allergy friendly chocolate chips.
- Vegetable Oil- We use 4 tablespoons in the ganache center so that the cookies do not need to be kept in the fridge.
- 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 into Vegan Chocolate Cookies
- 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.
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.
For Chocolate Ganache with Butter
- Use 4 tablespoons of unsalted butter instead of vegetable oil.
- Cookies must then be stored in the fridge and not at room temperature.
This recipe has not been tested with some of 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 chocolate filled cookies!
Step 1: Whisk Together the Dry Ingredients
In a large bowl, whisk together the gluten free flour, cocoa powder and salt. Set aside.
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 Butter and Sugar
Beat the butter and sugar together 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. The mixture will be chunky; that's normal.
Step 5: Add the Flour Mixture and Milk, Form into a Disc and Freeze
Starting and ending with the gluten free flour mixture, alternate between slowly beating in the gluten free flour mixture and milk 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 for it to come together.
Shape into a round flat disc, wrap in plastic wrap and freeze for 30 minutes.
Step 6: Scoop the Dough and Coat in Sugar
Using a small cookie scoop (or roll the dough into 1 inch balls), scoop the dough out into 40 scoops.
Drop the dough balls one at a time into the granulated sugar and coat completely.
Step 7: Make the Wells and Re-coat in Sugar
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.
Once again, drop each cookie into the granulated sugar and coat completely.
Step 8: Bake the Cookies
Bake the cookies in the center rack of the oven at 325 degrees Fahrenheit for 13 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.
Step 9: Make the Ganache
Place the chocolate chips, vegetable oil and corn syrup in a microwave safe bowl. Heat in 15 second increments, stirring after each time, until completely melted and incorporated.
Step 10: Fill the Cookies
Use a tiny spoon to pour the chocolate ganache into each hole of each cookie.
Expert Baking Tips
- Use Packed Cups of Flour- Normally in baking we do not use packed cups however, when working with gluten free, I've found using packed cups works best to help the baked goods keep their shape.
- 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 freeze the dough for at least 30 minutes, 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. Use a spatula to push them back into a circle shape. Work quickly because they harden pretty fast. If they are slightly puffed up, use the spatula to gently push them down and fix the center hole with the bottom of a wooden spoon.
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.
Storing: 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.
More Chocolate Cookie Recipes You'll Love
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📖 Recipe
Chocolate Thumbprint Cookies
Ingredients
For the Chocolate Cookies
- 2 ⅔ cups multipurpose gluten free flour (I use a gluten free multipurpose flour with xanthan gum already in it)
- 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
- 2 rounded tablespoons cornstarch mixed with 3 tablespoons water
- 1 cup unsalted butter or vegan baking stick, room temperature
- 1 ¼ cups granulated sugar , reserve ¼ cup for rolling
- 2 teaspoons pure vanilla extract
- ⅓ cup milk
For the Chocolate Ganache
- ¾ cup semi sweet chocolate chips
- 4 tablespoons vegetable oil
- 1 ½ teaspoons light corn syrup
Instructions
- In a large bowl, using a whisk, mix together the 2 ⅔ cups multipurpose gluten free flour, ⅓ cup cocoa powder and ½ teaspoon kosher salt. Set aside.
- In a small bowl, using a spoon, mix together the 2 rounded tablespoons cornstarch and 3 tablespoons 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 1 cup unsalted butter or vegan baking stick with 1 cup of the granulated sugar until soft and fluffy. About 2-3 minutes.
- Slowly beat in the cornstarch water mixture and 2 teaspoons pure vanilla extract into the butter and sugar until combined.
- Starting and ending with the gluten free flour mixture, alternate between slowly beating in the gluten free flour mixture and the ⅓ cup milk 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.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.There should be 40 dough balls total.Pour the ¼ cup of granulated sugar into a bowl. Drop each dough ball into the sugar and coat completely.
- 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.Re-drop each cookie into the granulated sugar and coat again.
- Place the cookies on the baking sheet about 2-3 inches apart.Bake the cookies in the center rack of the oven at 325 degrees Fahrenheit for 13 minutes.I bake no more than 12-15 at a time. Pop the extra dough balls into the fridge while the first group are baking.
- 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 Chocolate Ganache
- Place ¾ cup chocolate chips, 4 tablespoons vegetable and 1 ½ teaspoons light 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 the cookies right away when they’re all gooey or wait till they’re cool when the filling solidifies. Either way they’re delicious!
Video
Notes
Nutrition
john says
This is my absolute favorite cookie!