Thumbprint Chocolate Filled Cookies

Thumbprint-style cookies are heavily underrated. These cookies are soft, chewy, and so easy to fill with whatever flavor your heart desires. Check out this amazing chocolate-filled thumbprint cookie recipe to make the best thumbprint cookies you’ll ever have.

These chocolate thumbprint cookies are super easy to make, and they’re filled with the most delicious chocolate filling. This is the perfect chocolate filled cookie recipe to make around the holidays for your whole family to enjoy!

With the best texture on the cookie and a super fudgy interior, you definitely won’t ever have chocolate-filled cookies as tasty as these ones. 

• How to make a delicious chocolate filling for your cookies. 
• The differences between Dutch-processed and regular cocoa powder (and why that's important).
• The best technique for making a perfect thumbprint crater.

If you love this cookie recipe, check out my free guide that gives you 10 super helpful tips for becoming a better baker.

These cookies with chocolate in the middle require less than 10 simple ingredients, allowing you to whip this recipe up in no time. 

All-purpose flour: Flour provides the structure for your cookies. The best way to measure flour is with a digital food scale. If you aren’t using a scale, follow these steps to measure your flour accurately:

1. Fluff up the flour using a spoon. 

2. Scoop the flour into the measuring cup.

3. Level off the top of the measuring cup with a knife to remove excess flour. 

If you want to make this recipe gluten-free, use a 1-to-1 gluten-free baking flour, like Bob’s Red Mill. 

Dutch-processed cocoa powder: I prefer to use Dutch processed cocoa powder because it provides a more rich taste compared to unsweetened cocoa powder. However, in the pinch, you can substitute it with natural unsweetened cocoa powder.

Baking Soda: Always make sure to check how fresh your baking soda is before using it. Baking soda is definitely one of those ingredients that can sit in your pantry for too long and lose its quality. You will need fresh baking soda to get the best rise on your cookies. 

To test the baking soda, mix ½ cup of hot water and ¼ teaspoon of white vinegar. If you pour ¼ teaspoon of baking soda into this mixture and you get a fizzing reaction, the baking soda is fresh. If there’s no reaction, it’s time to buy some new baking soda. 

Salt: For this cookie recipe, and most baking recipes, fine sea salt works best. The smaller the granule of salt, the better it will distribute throughout the dough. 

Butter: Be sure to use unsalted butter. If you have to substitute for unsalted butter, make sure to decrease the amount of salt you add to your cookies. Depending on your preference, you could eliminate the salt entirely if you’re using salted butter. The butter will also be used for the chocolate filling, so be extra cautious if using salted butter, and adjust how much salt you use to garnish. 

Brown sugar: Brown sugar has a more nutty and caramelized taste than granulated sugar. This will add a nicer depth of flavor to your cookies. If you are choosing to measure the brown sugar by volume instead of weight, be sure to pack down the sugar into the measuring device. 

Granulated sugar: Be sure to save some extra sugar to roll the rough in before baking. This gives the cookies a beautiful look.

Egg: All you need is one large egg for this recipe. The egg is used to bind your cookie dough together. 

Vanilla extract: Just a smidge of vanilla extract is all you need to level up the flavor of your cookies. The vanilla provides another layer of flavor for a beautifully balanced cookie. 

Semisweet chocolate morsels: These chocolate morsels are the key ingredient for the chocolate filling that sits beautifully in the thumbprint.

Maldon sea salt flakes: Flaky salt and cookies are an underrated combo. The best chocolate cookies are finished with just a pinch of flaky salt that beautifully contrasts the sweet and rich chocolate flavor. This is a completely optional garnish. 

1. Begin by whisking most of your dry ingredients together. Combine the flour, cocoa powder, baking soda, and salt. Use a medium bowl for this. It is important to whisk your dry ingredients before adding the wet ingredients because it guarantees that the ingredients are evenly distributed and there aren’t any clumps of one ingredient or another. 

2. Separately, in a large bowl or a stand mixer, combine the butter, brown sugar, and ¼ cup (50 grams) of granulated sugar. You can use a handheld mixer or a stand mixer on medium speed to beat these ingredients together. Be sure to use the paddle attachment on your stand mixer and let these ingredients mix for 2 minutes until it is light and fluffy. 

3. Once the sugars and butter are ready, add in the egg and vanilla extract, and continue to beat the mixture on medium speed. Once the mixture is fully formed, you can shut off the mixer. 

4. Scrape down the sides of the bowl to keep all the ingredients together in the bottom. Now, you want to add the dry ingredients in half at a time. After adding the first batch, mix on medium-low speed until it's fully incorporated. Then add the second batch, and let the dough form. 

5. The dough should be slightly sticky when it's done. Wrap the cookie dough in parchment paper or plastic wrap, and let it sit in the refrigerator for at least 3 hours or up to overnight. This will help the dough firm up and be ready for you to work and shape your cookies.

6. After the dough has rested, preheat the oven to 350ºF (175ºC). Additionally, pour 3 tablespoons (40 grams) of granulated sugar onto a shallow plate, and set aside. 

Remove the dough from the fridge, and begin to form your cookies. Start by making 2 tablespoon (26 gram) balls. When the balls are formed, roll the outside of the dough in the granulated sugar.

7. On a large baking sheet lined with a silicone baking mat or parchment paper, place the cookie dough balls 2 inches (5 centimeters apart). Then, use your thumb or the backend of a wooden spoon to make an indent in each cookie. If you see that your dough begins to crack on the outside, simply use your hands and fingers to push it back together. 

8. Bake the cookies on the middle rack of the oven for 12–14 minutes or until you see that the edges are set. Once ready, remove the cookies from the oven, and let them rest for 5 minutes. If you see that any of the centers have puffed up, use the end of a wooden spoon to push the indent back down. You will not want to use your thumb this time as the cookies will be very hot and can burn you. 

After 5 minutes, transfer the cookies to a cooling rack to allow them to fully cool. 

9. Add the semisweet chocolate morsels and the butter to a heat-safe glass bowl.

10. Place the bowl in the microwave, and let the mixture heat for 30 seconds at 50% (medium) power.

11. Stir the chocolate mixture, and heat for an additional 30 seconds on the same settings.

12. Repeat this process until the chocolate is fully melted. 

13. Using a spoon, scoop the chocolate, and fill each thumbprint hole with about 1–2 teaspoons of the melted chocolate filling.

14. If you want, sprinkle the top of the filling with Maldon sea salt flakes. Let the cookies sit on a wire cooling rack until the filling has firmed.