These pecan pie cookie cups with a soft shortbread cookie base are so good I feel like I could eat ten in one sitting but, alas, my rations have changed since having kids, because losing those extra pounds is a little more work than it was ten years ago. These delicious pecan pie cookie cups are just in time for the holidays and would make the perfect dessert to take to a Thanksgiving event or other hosting event. The shortbread cookie crust is less fuss than a pie crust and tastes just as delicious paired with the delicious pecan pie filling, which has been a family favorite for decades. You may also enjoy Amish Pumpkin custard pie, Reese’s peanut butter cookie cups or Amish pumpkin whoopie pies.
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Pecan Pie Cookie Cups (with shortbread crust)
Equipment
- muffin tins (linked below)
- Mixing bowls (linked below)
- measuring cups (linked below)
- Whisk (linked below)
Ingredients
Shortbread Cookie Crust:
- 12 tablespoons butter softened
- 3/4 cup granulated sugar
- 1 large egg
- 2 1/4 cups all purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon salt
- 1 teaspoon vanilla extract
Pecan Pie filling:
- 2 tablespoons butter softened
- 1/2 cup brown sugar
- 2 large eggs room temperature.
- 1/2 cup Karo (light corn syrup)
- 1/2 cup whole milk
- 2 teaspoons vanilla extract
- 1 cup chopped pecans
Instructions
Preheat the oven to 350:
- Cream the butter and sugar together for the shortbread crust, then add the egg and whisk until smooth. Add the flour, baking powder, salt and vanilla extract, mixing until the shortbread dough is well combined and smooth (the shortbread dough should be somewhat stiff and you should be able to easily roll it into a ball without the dough cracking or sticking). Chill the dough for 30 minutes, or until the dough is chilled through, yet still easy to work with.
- While the shortbread is chilling, cream the softened butter and brown sugar together for the pecan pie filling. Whisk in the room temperature eggs, then add the Karo, whole milk and vanilla extract, mixing until well combined.
- Once the shortbread dough is chilled, roll the dough into 14 balls (may have more or less depending on the size of your muffin tins). Press the balls into the greased muffin tins, creating a shell with a thicker layer at the base (around 1/4 inch thick) to prevent the filling from seeping through while baking. Crimp the edges of the cookie cups away from the muffin tins, then fill each cookie cup 1/4 full with the crushed pecans. Pour the pecan pie filling over the pecans, filling the cookie cups until almost full (the filling doesn't rise much).
- Bake the pecan pie cookie cups in the preheated oven for 20-30 minutes until the crust is golden and the pie filling is set (doesn't jiggle when shaken). Allow the cookie cups to cool, then enjoy!
Notes
Equipment needed for these pecan pie cookie cups with shortbread cookie crust:
- Muffin tins I like to use my non-stick muffin tins for these pecan pie cookie cups. I also like to use cooking spray to grease the tins before baking the cookie cups, this makes for easier removal of the baked cookie cups.
- Measuring cups Measuring cups and spoons are nice to have to ensure an accurate measurement of the ingredients needed for these pecan pie cookie cups. I also like to use a measuring cup with a pour spout for pouring the pecan pie filling over the pecans in the crust.
- Mixing bowls Mixing bowls are needed for containing the ingredients needed for the shortbread crust and the pecan pie filling.
- Whisk I like to use a whisk and a large baking spoon for combining the wet and dry ingredients needed in the shortbread crust and in the pecan pie filling.
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Ingredients needed for these pecan pie cookie cups: Butter, eggs, pecans, brown sugar, vanilla extract, baking powder, salt, all purpose flour, Karo (light corn syrup), sugar and whole milk.
Should Salted or unsalted butter be used for the shortbread crust?
Honestly, I always use salted butter simply because that is what I prefer in my baked goods and for sauteeing veggies etc. If you only have unsalted butter on hand, you can use it but may wish to add a pinch of extra salt to the shortbread cookie dough.

Step 1: Cream the butter and sugar together for the shortbread crust, then add the egg and whisk until smooth. Add the flour, baking powder, salt and vanilla extract, mixing until the shortbread dough is well combined and smooth (the shortbread dough should be somewhat stiff and you should be able to easily roll it into a ball without the dough breaking or sticking). Chill the dough for 30 minutes, or until the dough is chilled through, yet still easy to work with.
Why does the shortbread cookie dough need to be chilled?
Refrigerating the shortbread cookie dough for 30 minutes solidifies the butter in the shortbread crust and keeps the dough from softening too soon in the oven. In essence, a chilled shortbread crust creates a stronger base for the pecan pie filling and helps to prevent a soggy bottom from the filling leaking through the crust.

Step 2: While the shortbread is chilling, cream the softened butter and brown sugar together for the pecan pie filling. Whisk in the room temperature eggs, then add the Karo, whole milk and vanilla extract, mixing until well combined.
What is Karo?
Karo is a light corn syrup that has been favored by my family for decades in baked goods and our Amish peanut butter spread. Other brands of light corn syrup can also be used in this recipe, but in my opinion, the Karo brand makes some of the best baked goods! (not an ad for Karo, lol.)

Step 3: Once the shortbread dough is chilled, roll the dough into 14 balls (may have more or less depending on the size of your muffin tins). Press the balls into the greased muffin tins, creating a shell with a thicker layer at the base (around 1/4 inch thick) to prevent the filling from seeping through while baking. Crimp the edges of the cookie cups away from the muffin tins, then fill each cookie cup 1/4 full with the crushed pecans. Pour the pecan pie filling over the pecans, filling the cookie cups until almost full (the filling doesn’t rise much).
What happens if the crust is too thin at the bottom of the cookie cups?
If the cookie base is too thin at the bottom or has uneven sections where the dough is thin, the pecan pie filling will seep through. To prevent this, keep the dough a little thicker at the bottom and then thinner on the sides. I also like to crimp the top edges of the cookie cups away from the muffin tins to keep the cookie cups from adhering to the edge of the muffin tin once the cookie cups are baked.

Step 4: Bake the pecan pie cookie cups in the preheated oven for 20-30 minutes until the crust is golden and the pie filling is set (doesn’t jiggle when shaken). Do not overbake, and keep an eye on the cookie cups toward the end of the 20 minutes to keep the crust from browning too much.

Allow the cookie cups to cool, then serve and enjoy!
Storage options for these pecan pie cookie cups:
Keep these pecan pie cups refrigerated, and avoid setting them out at room temperature for more than several hours. You can also freeze these pecan pie cookie cups in an airtight container or plastic bags for several months.

Feel free to pin this recipe for later and don’t forget to tag me on Instagram to show off a photo of your own creation of these pecan pie cookie cups. Thank you for your support!