These deliciously autumnal apple butter thumbprint cookies have a soft and tender texture, plenty of cinnamon and pools of silky spiced apple butter.
Apple Butter Thumbprint Cookies
Now that the air is crisp, the sun is setting earlier, and the trees have hints of gold, red and orange, we know that fall is definitely here. Thanks to the changing seasons, we can start making all the sweet and spiced apple desserts, including classics like apple cake and apple crisp but also creative new fall desserts such as apple butter thumbprint cookies. These soft cookies have a cinnamon and sugar flavor that’s reminiscent of snickerdoodles, except that the centers are filled with delicious, cinnamon-flavored apple butter.
Pick up a jar of apple butter at the store or from your local apple orchard and stash it in the pantry so you can whip up these thumbprint cookies anytime. Kids love these as an after-school snack; or, box some to share with friends.
What is apple butter?
Despite the name, apple butter contains no butter at all. This sweet spread is made by simmering chopped apples with sugar and spices. It’s a process that sounds similar to making homemade applesauce, except the difference is that for apple butter, the fruit is simmered for a long time over low heat to remove more of the water from the mixture, which leaves a thicker, silkier fruit spread. (That silky texture is probably why it has “butter” in the name!) The flavors of apple and spices like cinnamon and nutmeg are more concentrated as well.
Ingredients for Apple Butter Thumbprint Cookies
- Butter: Use unsalted butter for these cookies. If you forgot to take it out ahead of time, soften butter fast by cutting it into cubes or shredding it.
- Cinnamon: Different types of cinnamon have different flavor intensities. Ceylon is mild, while Vietnamese is spicier. Use your favorite!
- Apple butter: Apple butter is similar to applesauce, but it’s smoother and has more concentrated flavors. Store-bought apple butter makes it easy to whip up these cookies.
- Brown sugar: A small amount of light brown sugar in the dough brings a little molasses flavor that accentuates the apple and cinnamon.
- Egg: One egg in the batter gives the cookies extra richness. It’s a good baking habit to always use room-temperature eggs for more consistent results.
- Flour: All-purpose flour is the best choice here. Measuring flour correctly is important for all cookie recipes.
- Confectioners’ sugar: I like to use fine confectioners’ sugar to sweeten the cookies and give them a tender texture.
- Vanilla extract: There are vanilla extract brands out there to fit every budget. Watch for sales and stock up for fall and holiday baking.
- Baking powder: A little baking powder helps give the cookies a lift, as well as a lighter texture, as they bake.
- Nutmeg: Add a dash of nutmeg to complete the fall flavors in these cookies. Use a Microplane for lots of kitchen tasks, including grating whole nutmeg.
- Salt: Adding just a small amount of salt to the cookie dough enhances the flavor of the entire cookie.
- Granulated sugar: Have a small amount of granulated sugar ready so you can roll the cookie dough balls before filling and baking them.
Directions
Step 1: Blend the wet ingredients

Beat the softened butter, confectioners’ sugar and brown sugar together at medium-high speed in the bowl of a stand mixer fitted with the paddle attachment. Scrape the bowl once or twice, and beat for two to three minutes or until the mixture is creamy. Blend in the egg and then the vanilla extract until combined.
Step 2: Finish the dough and chill

Whisk the flour, cinnamon, baking powder, salt and nutmeg together in a separate bowl. Blend this dry mixture into the butter-sugar mixture in two additions, and scrape the bowl as needed. Cover the bowl and chill the dough for 30 minutes.
Step 3: Shape the cookies

Preheat the oven to 325°F and line a 15x10x1-inch baking sheet with parchment. Pour granulated sugar into a small bowl. Roll the cookie dough into 24 balls. (Each ball is about 1 rounded tablespoon.) Then, flatten the balls slightly and roll them in the granulated sugar to coat them. Place them on the prepared baking sheet 2 inches apart.
Editor’s Tip: When rolling the dough into balls, make them very smooth all the way around. Any cracks in the dough will widen during baking and let the apple butter melt out, so seal them up.
Step 4: Fill the cookies

Press the back of a teaspoon measuring spoon into the center of each dough ball to make an indentation. Then, use your thumb and forefinger to pinch up the sides and make the well in the center larger and deeper. Spoon a teaspoon of apple butter into each center.
Editor’s Tip: Keep any unrolled dough in the fridge while you bake the cookies to keep it from warming up.
Step 5: Bake the cookies
Bake the cookies for 13 to 14 minutes or until the edges are set. Transfer them to a wire rack and let the cookies cool completely.

Apple Butter Thumbprint Cookie Variations
- Add crunchy nuts: Chopped nuts like pistachios, walnuts or almonds are delicious in these cookies. Fold them into the cookie dough or sprinkle them over the tops before baking.
- Top them with caramel: Bring the flavor of caramel apples to the cookies by drizzling a little salted caramel sauce over them once they’re cool.
How to Store Apple Butter Thumbprint Cookies
Once the apple butter thumbprint cookies are completely cool, transfer them to your favorite food storage container. To protect the flavor and quality of the apple butter, the cookies should be stored in the refrigerator.
How long do apple butter thumbprint cookies last?
When they’re kept chilled in an airtight container, the apple butter thumbprints will last for up to five days.
Can you freeze apple butter thumbprint cookies?
Yes, these apple butter thumbprint cookies can be frozen. In fact, this is a great way to keep them on hand and have a fall-flavored treat anytime! Stack the baked, cooled cookies in a freezer-proof container, with sheets of waxed paper or parchment between the layers. Seal the container tightly and store the cookies in the freezer for up to three months. To thaw, move the container to the fridge the night before you want to serve them.
Apple Butter Thumbprint Cookie Tips

How do you keep the cookies from spreading too much in the oven?
When cookies spread in the oven, it’s often because the cookie dough is too warm and the butter melts out, making the cookies lose their shape. Chilling the dough in the fridge for 30 minutes will firm up the butter in the dough. Remember to keep the extra dough in the fridge between batches. If, after shaping and filling the cookie dough balls, the dough seems overly soft or greasy, pop the baking sheet in the fridge to chill them again before baking.
Can you use homemade apple butter for thumbprint cookies?
Absolutely! While store-bought apple butter is a great choice when you want to make these thumbprint cookies in a hurry, the treats will be even more delicious if filled with a homemade version. Our apple butter recipe is made with apples, sugar and spices. Let it simmer and cook down in a slow cooker all day while you work or get other things done. The finished apple butter will last for two weeks in the fridge or for several months in the freezer.
Ingredients
- 1 cup butter, softened
- 3/4 cup confectioners' sugar
- 1/4 cup packed brown sugar
- 1 large egg, room temperature
- 2 teaspoons vanilla extract
- 2-1/2 cups all-purpose flour
- 1 tablespoon ground cinnamon
- 1 teaspoon baking powder
- 1/2 teaspoon salt
- Dash ground nutmeg
- Sugar, for coating
- 1/2 cup apple butter
Directions
- In the bowl of a stand mixer fitted with the paddle attachment, cream butter, confectioners’ sugar and brown sugar together on medium-high speed until the mixture is creamy, 2-3 minutes, scraping the sides of the bowl as needed. Beat in egg and vanilla extract until combined.
- In a small bowl, whisk together flour, cinnamon, baking powder, salt and nutmeg; slowly beat into the butter mixture, scraping the sides as needed. Cover; chill 30 minutes.
- Preheat oven to 325°. Line a 15x10x1-in. baking sheet with parchment paper.
- Pour sugar into a small bowl. Roll chilled cookie dough into tablespoonfuls. Flatten the balls slightly; coat with sugar. Place on prepared baking sheet 2 in. apart. Press a teaspoon measuring spoon into the centers of each cookie to make an indentation. Use your fingers to pinch up the sides. Spoon 1 teaspoon apple butter into each indentation.
- Bake 13-14 minutes or until the edges are set. Transfer to a wire rack; let cookies cool completely.