Apple Pie Thumbprint Cookies

Apple Pie Thumbprint Cookies – tender and chewy almond shortbread cookies filled with a sweet and spiced homemade apple pie filling, just like Panera Bread!

apple pie cookies on a plate with apples and cinnamon in the background

Have you been to Panera Bread yet to try their irresistible apple almond thumbprint cookies? They aren’t exactly pretty but in this case, looks are deceiving because these cookies are DELICIOUS. Apple pie + almond shortbread cookies are a match made in heaven.

Ever fell in love with something on a menu only to find out it’s a seasonal limited-time offer, never to be seen again? It’s literally the worst. I couldn’t risk losing these cookies, so I bought a few and got to work developing this copycat Panera recipe.
My version of Panera’s apple almond thumbprint cookies isn’t an exact match. However, these might even be better. I’m obsessed with these cookies and I am totally making them every fall! I hope that you make them and love them as much as I do. Enjoy.

apple pie thumbprint cookies on a wooden sheet close up


For the Apple Pie Filling:

  • Apples (peeled and diced into small cubes) – Be sure to use apples that are good for baking like Gala, Granny Smith, or Braeburn. I used a combination of Golden Delicious and Honeycrisp but any baking apple will work.
  • Lemon Juice – prevents oxidation and prevents the apples from browning as quickly.
  • Pie Spice – You can use a combination of cinnamon, ginger, clove, nutmeg – anything that you would put in apple-pie would work. I use Penzey’s pie spice but you can use any sweet spice blend you like.
  • Sugar – Granulated white sugar is best to use for the filling.
  • Butter – thickens the filling and adds richness to the flavor.
  • Water – activates to the cornstarch so it can thicken the filling.
  • Cornstarch – thickens the apple pie filling into a thick jam-like consistency.
  • Vanilla Bean Paste (or extract) – sweetens and enhances the flavor.

For the Almond Thumbprint Cookies:

  • Almond Flour – gives this thumbprint a soft, chewy and perfectly dense consistency.
  • Flour – All-purpose white flour is used to build the structure of these cookies.
  • Salt – Adding a small amount of salt to sweet foods enhances the sweetness.
  • Butter (room temperature) – softens the cookie dough and adds color and flavor.
  • Sugar – sweetens!
  • Almond Extract – adds delicious almond flavor to the cookies.
  • Vanilla Bean Paste (or extract) – A good quality vanilla will make these cookies next-level delicious.

How to Make – The Steps

apple pie thumbprint cookies on a parchment with powdered sugar

To make the Apple Pie Filling:

Step 1 Make the apple pie filling: In a large mixing bowl, add diced apples, lemon juice, pie spice, and sugar. Toss to coat apples and combine.

Step 2 Cook apples: In a large pan, over medium heat, melt the butter. When the butter has melted, add the coated apples to the pan and cook, stirring frequently, until the apples begin to caramelize and appear glossy (10 to 15 minutes). If the butter dries up, add a splash of water and continue cooking.

Step 3 Add cornstarch: In a small bowl, mix together a teaspoon of water and corn starch. If the pan is dry, add a teaspoon or two more of water. Then, add the corn starch mixture. Stir well.

Step 4 Finish and cool: Bring the apple pie filling to a boil, cook for an additional 30 seconds to 1 minute to activate the cornstarch, and then stir in the vanilla. Transfer mixture to a bowl and let cool completely.

To make the Almond Shortbread Cookies:

Step 5 Preheat and prep baking sheet: Preheat the oven to 350 degrees F. Line two baking sheets with parchment paper and set aside.

Step 6 Mix dry ingredients: In a medium mixing bowl, add almond flour, flour and salt. Whisk well to combine. Set aside.

Step 7 Mix wet ingredients: In the bowl of an electric mixer, add butter, sugar, almond extract and vanilla. Mix until smooth and well combined.

Step 8 Mix almond shortbread cookie dough: To the bowl with the wet ingredients, add the dry ingredient mixture and mix on low until the flour is just incorporated and the dough forms. Do not overmix.

Step 9 Shape cookies: Using a rounded tablespoon, shape the dough into rounded balls and place on the prepared baking sheet, leaving at least an inch in between each ball. Press your thumb into the center of each ball of dough, creating a well for the apple pie filling. If the dough cracks, just gently press it back together.

Step 10 Bake and finish cookies: Transfer the baking sheet to a preheated 350-degree oven and bake for 18 to 24 minutes or until the dough has been set but not yet browned. Allow the cookies to cool completely before filling each well with apple pie filling. Dust with powdered sugar (optional) and enjoy.

apple pie thumbprint cookies on a plate with apples and a mug in the background

Tips & Tricks

  • I start with the filling. It may seem tedious but dice the apples as small as you can. You want the filling to have some texture, but the pieces need to be small enough to fit in the cookie wells.
  • You can make the apple pie filling and store it in the fridge until you’re ready to fill the cookies. If you are really feeling it, double the apple pie filling and use the other half for spooning over ice cream, vanilla yogurt, or stirring into your morning oatmeal. 
  • I like my pie filling to be really spiced, so I am heavy-handed with the pie spice.
  • As with any type of cookie dough, be careful not to overmix the dough. You want a tender cookie, not a tough one.
  • When I first made these, I wasn’t crazy about the texture. However, I loosely covered them with plastic wrap, and the next morning they were perfect. That said, be sure to loosely cover the cookies with plastic wrap and let sit overnight before eating. The texture will be perfect the next day.
apple pie thumbprint cookies on a baking sheet

Why are Apple Pie Thumbprint Cookies So Good?

  • These cookies fuse all of the flavors and textures of homemade apple pie into a bite-size indulgent cookie.
  • Thumbprint cookies are a great addition to your holiday cookie baking list. They’re perfect for gifting and bringing to gatherings.
  • Made with simple ingredients yet packed with sweet, spiced, and cozy flavors.
  • Simple. Making thumbprint cookies is easier than it looks.
apple pie cookies on a plate

When it comes to thumbprint cookie flavors, the options are endless. In addition to this apple pie filling, almond thumbprint cookies are great filled with:

  • Raspberry Jam
  • Orange Marmalade
  • Strawberry Preserves
  • Chocolate Sauce
  • Caramel Sauce
  • Peanut Butter & Grape Jelly
apple pie cookies on a sheet being dusted with powdered sugar

How to Store

Storing: Store thumbprint cookies in an airtight container for up to a week at room temperature. The cookies will stray fresh for up to a week before they lose their moisture and become dry.

Make-Ahead and Freezer Options

Freezing: To freeze almond thumbprint cookies, freeze the shortbread cookie without the filling. You can add the filling once the cookies have thawed out.

apple pie thumbprint cookies on a plate with apples and a mug in the background


Why did my thumbprint cookies go flat?

If there isn’t enough flour in the dough to absorb the fat and moisture, your cookies will spread too much and become flat. Be sure to measure out the flour precisely or better yet, weigh the flour to ensure you’re using the right amount.

Should you fill thumbprint cookies before or after baking?

I recommend filling the cookies immediately after they are finished baking. You may need to gently re-indent the cookie.

Why aren’t my thumbprint cookies spreading?

Your cookies may not be spreading for a few reasons but the most common reason is that the dough isn’t the right temperature. The dough should be at room temperature at all times for the best shape and textured cookies.

More Cookies Recipes

Chewy Honey Gingerbread Cookies

Almond Cafe Cookies

Sunflower Seed Cookies

Molasses Spice Cookies

apple pie cookies on a plate

Apple Pie Thumbprint Cookies

4.53 from 21 votes
Prep Time 35 minutes
Cook Time 28 minutes
Total Time 1 hour 3 minutes
Course cookies
Cuisine fall baking
Servings 36 cookies
Calories 171 kcal


Apple Pie Filling:

  • 2 apples peeled and cut into a small dice
  • 1 Tablespoon lemon juice
  • 2 teaspoons pie spice
  • cup sugar
  • 2 Tablespoons butter
  • 1 teaspoon water
  • 1 teaspoon cornstarch
  • 1 teaspoon vanilla bean paste or extract

Almond Thumbprint Cookies:

  • 1 cup almond flour
  • 3 ½ cups flour
  • ½ teaspoon salt
  • 1 ½ cups butter room temperature
  • 1 cup sugar
  • 1 teaspoon almond extract
  • 1 teaspoon vanilla bean paste or extract


  • To make the filling, toss apples, lemon juice, pie spice, and sugar in a bowl. 
  • Melt butter in a saute pan over medium heat. Add the apples and stir to coat with butter. Let the apples cook for 10 to 15 minutes. If the pan gets too dry, add a tablespoon or two of water. 
  • When the apples begin to caramelize and get glossy, add ¼ cup water if the liquid has evaporated. Mix together a teaspoon of water and a teaspoon of cornstarch and add to the pan. 
  • Stir and bring the apple mixture to a boil. Cook for another 30 seconds to a minute more for the cornstarch to activate. Stir in vanilla bean paste. Transfer to a bowl and let cool completely. 
  • To make the almond thumbprints, preheat the oven to 350°. Line two baking sheets with parchment paper and set aside. 
  • Whisk together almond flour, flour, and salt in a medium bowl and set aside. 
  • In the bowl of an electric mixer, mix together butter, sugar, almond extract, and vanilla bean paste until smooth and combined. 
  • Add the almond flour mixture and mix on low until the flour is just incorporated and the dough comes together. 
  • Divide the dough using a tablespoon scoop. Place on baking sheet an inch apart. Make a well using your thumb. If the cookies crack, just press them back together. 
  • Bake the cookies for 18 to 23 minutes. You want them to be set, but not browned. Take out of the oven let cool on a wire rack. Dust with powdered sugar and fill with apple pie filling.



Serving: 1gCalories: 171kcalCarbohydrates: 19gProtein: 2gFat: 10gSaturated Fat: 5gPolyunsaturated Fat: 4gCholesterol: 22mgSodium: 96mgFiber: 1gSugar: 9g
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