Apple Pie Thumbprint Cookies

apple pie thumbprint cookies on  a baking sheet close up

Apple Pie Thumbprint Cookies – a copycat Panera Bread almond-scented shortbread cookie filled with a delicious spiced filling.

apple pie thumbprint cookies on a parchment with powdered sugar

Have you been to Panera lately and had their apple almond thumbprint cookie? They aren’t the prettiest cookie I’ve ever seen, but let me tell you, they are DELICIOUS. I love apple pie and I love cookies, these are a match made in heaven.

I bought a few and brought them home to try to re-create them. You know how you fall in love with something somewhere, but it’s a limited edition or seasonal, never to be seen again? I don’t want to lose these cookies from my life. 

I created this version and while it isn’t 100% exact, they might be even better. These are so good, I’m obsessed with them. 

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

I start by making the filling. It might seem tedious, but dice the apples as small as you can. You want the filling to have some texture, but it also needs to be small enough to fit in the indents. 

I like mine to be really spiced, so I am heavy-handed with the pie spice. If you are really feeling it, double the apple pie filling and use the other half for spooning over ice cream, add it to some vanilla yogurt, or stirring into your morning oatmeal. 

almonf thumbprint cookies on a baking sheet

When I first made these, I didn’t like them. I thought that they were too crisp and not chewy enough. I told my husband to take them to school (his graduate students are getting a lot of baked goods these days) and loosely covered the baking sheet with plastic wrap. The next morning I was packing them up, tried one again, and it was EXACTLY what I was going for.

Letting them rest overnight made the apple flavor develop and let the cookies soften a bit. Not soggy by any means, but it changed the texture into exactly what I wanted it to be. 

These are absolutely delicious and going to be making an appearance every fall in my house. I can skip the Panera and just make a batch myself.

Cookies on a sheet being dusted with powdered sugar

Tips for making the best apple pie cookies //

  • When making the shortbread, be careful to not overmix the dough. You want a tender cookie, not a tough one. 
  • The filling recipe can be doubled and used for other things – top anything that could use some apple pie flavor. 
  • These cookies taste better the next day. Loosely cover the cookies with plastic wrap and let sit overnight before eating. 
  • I used a combination of Golden Delicious and Honeycrisp, but any baking apple will work.
  • The filling can be made ahead of time stored in an airtight container in the fridge.
  • If you don’t want to make an apple pie version, add your favorite jam to the well before baking.
  • I use Penzey’s pie spice, but you can use any spice blend you like.

cookies on a plate

These cookies are so good, I hope that you make them and love them as much as I do.

apple pie cookies on a plate

Apple Pie Thumbprint Cookies

Yield: 36 cookies
Prep Time: 35 minutes
Cook Time: 28 minutes
Total Time: 1 hour 3 minutes

Apple Pie Thumbprint Cookies - an almond-scented shortbread thumbprint cookie filled with a delicious spiced apple pie filling. 


Apple Pie Filling:

  • 2 apples, peeled and cut into a small dice
  • 1 Tablespoon lemon juice
  • 2 teaspoons pie spice
  • ⅓ 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


  1. To make the filling, toss apples, lemon juice, pie spice, and sugar in a bowl. 
  2. 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. 
  3. 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. 
  4. 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. 
  5. To make the almond thumbprints, preheat the oven to 350°. Line two baking sheets with parchment paper and set aside. 
  6. Whisk together almond flour, flour, and salt in a medium bowl and set aside. 
  7. In the bowl of an electric mixer, mix together butter, sugar, almond extract, and vanilla bean paste until smooth and combined. 
  8. Add the almond flour mixture and mix on low until the flour is just incorporated and the dough comes together. 
  9. 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. 
  10. 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.


Thumbprint cookies adapted from King Arthur Flour.

Nutrition Information:
Yield: 36 Serving Size: 1
Amount Per Serving: Calories: 171Total Fat: 10gSaturated Fat: 5gTrans Fat: 0gUnsaturated Fat: 4gCholesterol: 22mgSodium: 96mgCarbohydrates: 19gFiber: 1gSugar: 9gProtein: 2g

Did you make this recipe?

Please leave a comment on the blog or share a photo on Pinterest

Oh hey there!

Well, hello there! I’m Bree Hester, the Boston-based blogger and food photographer here at Baked Bree. Here you can get lots of weeknight meal inspiration, eat more plant-based meals, and still indulge in a decadent sweet treat. Baked Bree is a place where you will find great recipes and inspiration for your next family adventure.

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This Post Has 6 Comments

  1. Zoe

    Hi Bree
    I live in Fiji so I won’t be able to buy any pie spice.
    These cookies sound delicious though and I would love to make them.
    Please can you let me know how I could mix a similar pie spice at home that I could then use?
    Thank you!

    1. Bree Hester

      I hope that you do! You can use a combination of cinnamon, ginger, clove, nutmeg – anything that you would put in apple pie would work.

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