Thumbprint cookies are the ultimate versatile treat. You can fill them with pretty much anything from jam to nut butter to chocolate and even candy – the options are endless!
These apple pie thumbprint cookies are a delicious, fall-inspired twist that’s a little softer, juicier, and full of warm spices.
With a healthier base made from wholemeal flour and coconut sugar, they’re chewy, lightly sweet, and balanced perfectly by the gooey apple pie filling.
A drizzle of icing on top makes them quite festive, so they’re perfect for Thanksgiving or any holiday cookie plate this fall season.
What You’ll Need
This recipe has three parts:
The cookies are made with wholemeal flour, cornstarch that helps keep them soft, melted butter, eggs, almond extract, and coconut sugar for that caramel flavor.
The apple pie filling: diced apples are cooked with butter, coconut sugar, lemon juice, cinnamon, and a dash of pumpkin spice until soft and syrupy.
The optional icing is a simple mix of powdered sugar, milk, lemon juice, and vanilla that you can drizzle over the top for extra flavor and decoration.
How to Make These Apple Pie Thumbprint Cookies
Start by making the cookie dough:
Melt the butter and let it cool slightly. In a large bowl, whisk together the flour, cornstarch, baking powder, and salt. Set aside.
In another bowl, mix the melted butter, eggs, and almond extract until smooth. Stir in the coconut sugar and whisk until well blended.
Combine wet and dry ingredients until you have a thick, sticky dough. Chill it in the fridge for at least 30 minutes to make the dough easier to shape.
While the dough chills, peel and dice the apples into small cubes. Melt butter in a pot, then add apples, lemon juice, cornstarch, sugar, cinnamon, and pumpkin spice. Cook until the apples soften and the mixture thickens into a glossy filling. Let it cool completely.
When the dough is chilled, scoop out tablespoon-sized portions of dough and roll them into smooth balls. Place on a parchment-lined baking tray, leaving room between each.
Use your thumb or index finger to press gently into the center of each ball, making a small well for the filling. The dough will flatten and expand slightly, so you can reshape the cookies if they become too flat.
Bake the cookies at 350°F for 10–12 minutes, until the bottoms turn lightly golden. Take them out and, while still warm, press into the centers again to keep the indentations defined. Don’t skip this step!
When the cookies have cooled, spoon the apple pie filling into each cookie center and you’re done!
If you like, whip up a quick icing by mixing powdered sugar, milk, lemon juice, and vanilla until smooth. Drizzle lightly over the cookies and let the icing set for a couple of hours before serving.
Why You’ll Love This Recipe
- Full of fall flavors: This recipe uses a cinnamon apple pie filling inside caramel-ly thumbprint cookies instead of more classic fillings like jam or chocolate.
- It’s got a healthier base: The cookies are made with wholemeal flour and coconut sugar instead of white flour and regular sugar.
- The cookies come out looking cute and festive: They’re perfect for fall baking, holiday cookie swaps, or Thanksgiving dessert tables.
- Soft and chewy on the inside: Cornstarch keeps the cookies tender on the inside and the apple filling makes the cookies more juicy and moist, too.
- Easily customizable: Skip the icing for a simpler version, or add some crunch with nuts.
Tips for Success
- Make sure to chill the dough first – this helps prevent the cookies from spreading too much.
- Re-indent after baking so the cookies retain their thumbprint shape and filling sits nicely in the cookies.
- Cool the filling before using or it will melt into the cookies.
- Don’t overbake! Around 10 minutes is enough – these cookies are best soft, not crunchy.
- Decorate them as you like: drizzle icing, dust with cinnamon, or even add chopped nuts on top.
📌 Apple Pie Thumbprint Cookies (Recipe Card)
Ingredients (Makes 20 cookies)
Cookies
- 2 cups wholemeal flour
- 2 teaspoons cornstarch
- 1 1/2 teaspoons baking powder
- Pinch of salt
- 3 tablespoons butter, melted
- 2 eggs
- 1 teaspoon almond extract
- 3/4 cup coconut sugar
Apple Pie Filling
- 1 1/2 tablespoons butter
- 2 medium apples, peeled and diced
- 1 tablespoon lemon juice
- 1 tablespoon cornstarch
- 3 tablespoons coconut sugar
- 1 teaspoon cinnamon
- Dash of pumpkin spice
Icing (optional)
- 1/2 cup powdered sugar
- 1 tablespoon milk
- Splash of lemon juice
- Few drops of vanilla extract
Equipment
- Mixing bowls
- Hand whisk or mixer
- Saucepan for filling
- Baking tray
- Parchment paper
Instructions
- Melt butter in a small pot and let it cool.
- In one bowl, whisk together flour, cornstarch, baking powder, and salt until well combined.
- In another bowl, beat butter, eggs, and almond extract until smooth. Stir in coconut sugar and mix again.
- Combine wet and dry ingredients to form a thick, sticky dough. Refrigerate for at least 30 minutes.
- To make the filling, melt butter in a saucepan. Add diced apples, lemon juice, cornstarch, coconut sugar, cinnamon, and pumpkin spice. Cook until apples are soft and the mixture thickens. Cool completely.
- Preheat oven to 350°F. Line a tray with parchment paper.
- Roll dough into 20 balls. Place on a baking tray about a quarter-inch apart and press a thumbprint into the center of each ball. You may need to use two baking trays.
- Bake for 10–12 minutes until lightly golden. While warm, press centers again to maintain shape. Cool on tray.
- Fill indentations with cooled apple pie filling.
- Optional: mix powdered sugar, milk, lemon juice, and vanilla until smooth. Drizzle over cookies and serve once icing sets (this will take a couple of hours).
