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    Home » Desserts » Cookies

    Published Aug 7, 2023 (Updated Feb 19, 2025) by Heather Bilyeu

    Tender Apple Pie Thumbprint Cookies

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    Apple pie thumbprint cookies are the perfect sweet treat to enjoy this fall! Loaded with a homemade apple pie filling tucked in a tender spiced cookie. Baked at 350 for 11 minutes, these are a mini handheld version of the classic fall pie in cookie form!

    I know that all pumpkin everything is all the rage this time of year, but in my opinion, apple-flavored treats are highly underrated!

    My body craves a crisp apple in season in the fall and I love baking with apples. From My Mom's Apple Pie Recipe, Apple Bundt Cake with Bourbon Caramel Glaze, 4 Ingredient Apple Dip to Brown Butter Apple Bars and now cookies! We are taking all the classic flavors of apple pie and putting them in cookie form and you will not be upset!

    A hand grabbing an Apple Pie Thumbprint Cookies off a plate of them.
    Clear bowls of flour, sugar, apples, spices, egg, butter, and vanilla.

    How to Make

    Step One: Make the Spiced Cookie Dough

    1. In a stand mixer, add butter and sugar and mix for 5 minutes until light and fluffy.
    2. Add in egg and vanilla and mix until just combined.
    3. Add in flour, baking powder, and spices. Mix just until the dough has come together and everything is combined.
    4. Scoop out cookie dough with a cookie scoop onto a baking sheet lined with parchment paper.
    5. In a medium bowl, mix together the sugar and cinnamon. Roll each dough ball in the cinnamon and sugar. Place back on the cookie sheet and repeat with all the dough balls.
    6. With a half-tablespoon round measuring spoon or wooden spoon, gently press a round circle divet in the middle of each dough ball. Do not press all the way down to the bottom, but just enough to create a hole for the filling to fit in. If the dough cracks around the edge, press it back together with your fingers. Place in the fridge and chill for at least an hour (or up to 24 hours).
    Rolling cookie dough in cinnamon and sugar with intending them with a spoon for a hole in the middle.
    I like to use a ½ Tablespoon spoon to gently indent the thumbprints in the cookies after they have been rolled in cinnamon sugar. You can also use the end of a wooden spoon or your thumb to make the indention.

    Step Two: Make the Apple Pie Filling

    1. While the dough is chilling, finely dice the apples into small pieces. Dice as small tiny squares as possible so that they will fit in the center of the circle. You do not need to peel the skin off. 
    2. Place the diced apples in a skillet with the butter, sugars, and spices. Cook on medium for 5-10 minutes until the butter is melted and the apples have cooked and softened. Remove from the heat until needed.
    apple pie filling in a clear bowl
    You want to diced the apples into small pieces so that they can fit into the cookies easily.
    apple pie filling mixed up in a clear bowl
    Toss together with the sugars and spices to create a small batch of apple pie filling.

    Step Three: Assembled, Bake, and EAT!

    1. Preheat the oven to 350 degrees.
    2. Place 12 cookies on a baking sheet lined with parchment paper. Spoon about a ½-1 teaspoon of apple filling in the middle hole of each dough ball - filling as much of it as it will hold.
    3. Place in the oven to bake for 11-12 minutes.
    4. Remove and let cool for 5 minutes on the cookie sheet, then move to a cooling rack to finish cooling.
    1 apple pie thumbprint cookies on a green table with a napkin and cinnamon sticks around it.

    Helpful Tips

    Thumbprint cookies can be a bit tricky. This took me several rounds of recipe testing to get just right. During my testing, I learned a couple of helpful tips for you along the way.

    • Dice the apples as small as possible. I know this is a bit tedious, but it is crucial. I took the extra time to finely dice the apples into tiny squares and it made all the difference! Because the holes in the cookies aren't that big, having finely diced apples helps them sit tucked in the holes nicely and is easy to eat.
    • Do not over-mix the dough. This dough is on the "thicker" side with a bit more flour so they don't spread too much to maintain the integrity of the thumbprint holes. If you overmix the dough, it will result in a dry and crumbly dough. Mix everything until just combined.
    • Follow the steps in order. Because the dough needs to chill, make the dough first, then the filling, then assemble and bake. It is the most efficient use of your time.

    How to Make Apple Pie Thumbprint Cookies Ahead and Freeze: You know I love freezing cookie dough! Make the cookie dough all the way up to step 6. Place in the freezer for 30 minutes. Place frozen cookie dough in a freezer-safe container for up to 6 months. To bake, make the apple pie filling and place it in frozen cookie dough. Bake at 350 for 12-13 minutes.

    A green platter of Apple Pie Thumbprint Cookies with apples in the background.
    Broken and unbroken Apple Pie Thumbprint Cookies on a green table with apples, cinnamon sticks, and a napkin all around them.
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    Recipe

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    apple pie thumbprint cookies on a green plate with apples, napkins, and cinnamon sticks around it.

    Tender Apple Pie Thumbprint Cookies


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    • Author: Heather Bilyeu
    • Total Time: 1 hour 42 minutes
    • Yield: 28 cookies
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    Description

    Apple pie thumbprint cookies are the perfect sweet treat to enjoy this fall! Loaded with a homemade apple pie filling tucked in a tender spiced cookie. Baked at 350 for 11 minutes, these are a mini handheld version of the classic fall pie in cookie form!


    Ingredients

    Scale

    Spiced Cookie Dough

    • 1 Cup Butter - room temperature
    • ¾ Cup Sugar
    • 1 Egg
    • 1 Teaspoon Vanilla Bean Paste 
    • 2 ¼ Cup Flour
    • 1 Teaspoon Baking Powder
    • ½ Teaspoon Cinnamon
    • ¼ Teaspoon Nutmeg
    • ¼ Teaspoon Cloves
    • ¼ Teaspoon Salt
    • ½ Cup Sugar + ½ Tablespoon Cinnamon for rolling dough in

    Apple Pie Filling

    • 2 Medium Honeycrisp Apples - finely diced
    • 4 Tablespoons Butter
    • 2 Tablespoons Sugar
    • 2 Tablespoon Brown Sugar
    • 2 Teaspoon Corn Starch
    • 1 Teaspoon Cinnamon
    • ½ Teaspoon Nutmeg
    • ½ Teaspoon Cloves


    Instructions

    Spiced Cookie Dough

    1. In a stand mixer, add butter and sugar and mix for 5 minutes until light and fluffy.
    2. Add in egg and vanilla and mix until just combined.
    3. Add in flour, baking powder, and spices. Mix just until the dough has come together and everything is combined.
    4. Scoop out cookie dough with a cookie scoop onto a baking sheet lined with parchment paper.
    5. In a medium bowl, mix together the sugar and cinnamon. Roll each dough ball in the cinnamon and sugar. Place back on the cookie sheet and repeat with all the dough balls.
    6. With a half-tablespoon round measuring spoon or wooden spoon, gently press a round circle divet in the middle of each dough ball. Do not press all the way down to the bottom, but just enough to create a hole for the filling to fit in. If the dough cracks around the edge, press it back together with your fingers. Place in the fridge and chill for at least an hour (or up to 24 hours).

    Apple Pie Filling

    1. While the dough is chilling, finely dice the apples into small pieces. Dice as small tiny squares as possible so that they will fit in the center of the circle. You do not need to peel the skin off. 
    2. Place the diced apples in a skillet with the butter, sugars, and spices. Cook on medium for 5-10 minutes until the butter is melted and the apples have cooked and softened. Remove from the heat until needed.

    Assembly

    1. Preheat the oven to 350 degrees.
    2. Place 12 cookies on a baking sheet lined with parchment paper. Spoon about a ½-1 teaspoon of apple filling in the middle hole of each dough ball - filling as much of it as it will hold.
    3. Place in the oven to bake for 11-12 minutes.
    4. Remove and let cool for 5 minutes on the cookie sheet, then move to a cooling rack to finish cooling.

    Notes

    • Granny Smith or Honeycrisp Apples are the preferred/best apples to use for this recipe.
    • Store leftovers in the fridge covered for 3 days. 
    • See the post for how to make ahead and freeze. 
    • 1 teaspoon of vanilla extract can be used in place of vanilla bean paste if you do not have it.
    • Prep Time: 30 minutes
    • 1 hour:
    • Cook Time: 12 minutes
    • Category: Dessert
    • Method: Baking
    • Cuisine: American

    Nutrition

    • Serving Size: 1 cookie
    • Calories: 148
    • Sugar: 8.4 g
    • Sodium: 25.5 mg
    • Fat: 8.5 g
    • Carbohydrates: 17 g
    • Fiber: 0.7 g
    • Protein: 1.4 g
    • Cholesterol: 28.4 mg

    Did you make this recipe?

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    Filed Under: Cookies, Fall, Halloween, Recipe Video, Thanksgiving Tagged With: Apples

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    Hi, I'm Heather! Grab a glass of wine, a blanket, and a cozy seat on your back porch. I am so glad you are here! Born and raised in Kentucky and with proper southern roots, my love for entertaining and hospitality runs deep within my soul. There is nothing that I love more than having people around my table and loving them through food and drink!

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