If you love pecan pie and you’re looking for a unique cookie recipe that combines the best of both worlds, these pecan pie sourdough cookies are about to become your new favorite fall and holiday treat. These aren’t your average cookies, they’re part of my beloved upside down cookie series, where I take classic desserts and transform them into stunning, layered cookies with a beautiful marbled effect.
These long-fermented sourdough cookies feature a soft, tangy cookie base, a buttery cinnamon crumble, and a rich pecan pie filling that tastes just like the real thing. The secret? We bake them upside down, creating that gorgeous marbled top and keeping the cookie base incredibly soft and tender.
Jump to:
- What Makes These Pecan Pie Cookies Special
- Tips for Perfect Cookies
- Why Toast the Pecans
- Troubleshooting
- FAQs
- Nutrition Information
- More Upside Down Cookie Recipes
Pecan Pie Sourdough Cookies
Equipment
- Large mixing bowl
- medium mixing bowl
- Food processor (or pastry cutter for hand method)
- Rubber spatula or wooden spoon
- Whisk
- Rolling Pin
- 2.5-3 inch circle cutter or wide mouth canning jar
- Large baking sheet
- Parchment paper
- plastic wrap
- kitchen scale Measuring cups and spoons
- Medium saucepan
Ingredients
Sourdough Cookie Base:
- 120 g active sourdough starter bubbly and ready to use
- 113 g unsalted butter softened (room temperature)
- 80 g powdered sugar
- 67 g brown sugar
- 50 g egg 1 large
- 5 g vanilla extract
- 270 g all-purpose flour
- 2 g baking powder 1/2 teaspoon
- 1.5 g salt 1/4 teaspoon
- 1/8 teaspoon cream of tartar
Fermented Crumble Topping:
- 120 g all-purpose flour
- 80 g brown sugar
- 30 g active sourdough starter
- 60 g unsalted butter cold and cubed
- 1/2 teaspoon salt
- 5 g vanilla extract
- 30 g powdered sugar
- 1/2 teaspoon cinnamon
Pecan Pie Filling:
- 200 g pecans roughly chopped (some left larger for visual appeal)
- 130 g brown sugar
- 70 g unsalted butter melted
- 65 g egg 1 large egg + 1 tablespoon, or 1 large egg
- 40 g cornstarch
- 40 g heavy cream or milk
- 5 g vanilla extract
- 1/4 teaspoon salt
- 1/4 teaspoon cinnamon optional
Optional Drizzle:
- 100 g white chocolate or caramel for drizzling
Instructions
Day 1: Prepare Dough and Crumble for Fermentation
Make the Cookie Dough:
- In a large bowl, cream together softened butter, powdered sugar, and brown sugar until light and fluffy (about 2-3 minutes).
- Add egg and vanilla extract, mix well until combined.
- Add sourdough starter and mix until fully incorporated.
- In a separate bowl, whisk together flour, baking powder, salt, and cream of tartar.
- Gradually add dry ingredients to wet ingredients, mixing until just combined. Don’t overmix!
- Dump dough onto plastic wrap, wrap well, and refrigerate for 8-24 hours.
Make the Fermented Crumble (Food Processor Method):
- Add flour, brown sugar, salt, powdered sugar, cinnamon, and sourdough starter to food processor.
- Pulse 3-4 times to combine dry ingredients.
- Add cold cubed butter and pulse 10-15 times in short bursts until mixture resembles coarse crumbs.
- Add vanilla and pulse 1-2 times just to incorporate.
- Continue pulsing until you have a brown sugar-like texture that holds together when squeezed but isn’t a dough ball. Go slowly!
- Cover and refrigerate alongside the cookie dough for 8-24 hours.
Day 2: Assembly and Baking
Prepare the Pecan Pie Filling:
- Optional but recommended: Toast the chopped pecans in a dry medium saucepan over medium heat for 3-5 minutes, stirring frequently, until fragrant and slightly darkened. Transfer to a bowl and set aside.
- In a medium bowl, whisk together melted butter, brown sugar, egg, heavy cream, cornstarch, vanilla extract, salt, and cinnamon (if using) until smooth and well combined.
- Fold in the chopped pecans (toasted or untoasted).
- Transfer mixture to a medium saucepan and cook over medium-low heat, stirring constantly, for 5-8 minutes until mixture thickens significantly to a thick custard consistency. The filling should be thick enough that when you drag a spoon through it, it holds its shape and doesn’t immediately flow back together.
- Remove from heat and let cool completely (at least 45 minutes). Cover with plastic wrap pressed directly on the surface and refrigerate until cold. The filling must be completely cool before assembly.
Prepare for Assembly:
- Preheat oven to 350°F (175°C).
- Line a large baking sheet with parchment paper.
- Get your 2.5-3 inch circle cutter or wide mouth canning jar ready.
Assemble the Cookies:
- Using your circle cutter as a guide, spread about 2 rounded tablespoons of fermented crumble mixture on the parchment in circles. Don’t press them together or down. Just loosely arrange in a circle the size of the cutter. Leave small gaps in the crumble for the marbled effect!
- Top each crumble circle with 1 rounded tablespoon of cooled pecan pie filling. Gently spread around the middle, keeping it from going over the edges of the crumble.
- Tip: You can take your ball of pecan filling and flatten out into a disk, then place in the middle of the crumble layout.
- Roll out the fermented cookie dough on a floured surface to a rough rectangle, 12” × 10”, approximately 3/8” thick. (The line between 1/4" and 1/2"
- Using your circle cutter, cut out circles from the dough.
- Gently gather scraps, press together to form a ball, and roll out another rectangle. Continue cutting until all dough is used. If the dough resists, wrap and refrigerate for 15-30 minutes.
- Place each cookie circle on top of the crumble and pecan pie layers.
- Gently press down to adhere, making sure the crumble and pecan filling are under the cookie.
- Push any crumble sticking out from under the cookie top back underneath to keep the edges tidy.
Bake:
- Bake for 18-22 minutes, until you can see dark golden browning on the crumble edges around the bottom.
- Remove from oven and let cool completely on the baking sheet for at least 1 hour. Don’t rush this step! The cooling time allows the cornstarch mixture and crumble to set properly.
Add Drizzle (Optional):
- Melt white chocolate with a teaspoon of coconut oil, or warm caramel, until smooth and drizzle-able.
- Using a spoon or piping bag, drizzle over the cooled cookies.
Notes
What Makes These Pecan Pie Cookies So Special?
The Upside Down Cookie Method
If you’ve followed along with my upside down cookie series, you know this technique creates something truly magical. We start by laying down a fermented crumble, top it with pecan pie filling, then cover it with a circle of sourdough cookie dough. When baked upside down, the crumble and filling peek through the top, creating a stunning marbled effect that looks as impressive as it tastes.
I’ve used this method for s’more cookies, peach pie cookies, blueberry pie cookies, apple pie cookies, strawberry shortcake cookies, and cherry pie cookies and this pecan pie version might just be the favorite yet.
Why Sourdough?
The long fermentation (8-24 hours) does incredible things to these cookies:
- Develops complex flavor that balances the sweetness of the pecan filling
- Creates a tender, melt-in-your-mouth texture
- Makes the cookies easier to digest
- Adds that signature sourdough depth
The Pecan Pie Filling
This isn’t just pecan pie filling, it’s been specially formulated to stay put during baking. With the perfect ratio of cornstarch, butter, and cream, it thickens into a rich custard that won’t leak or spread beyond the cookie edges. Toasted pecans add nutty depth and that authentic pecan pie flavor.
Tips for Perfect Pecan Pie Sourdough Cookies
Getting That Marbled Effect:
- Leave gaps in the crumble layer when spreading it on the parchment. The pecan filling peeking through is what creates the beautiful marbled top.
- Use contrasting colors, the golden crumble against the darker pecan filling makes the marble effect pop.
Assembly Tips:
- Make sure all components are completely cool before assembly, especially the pecan filling.
- Push stray crumbs underneath the cookie top for clean, uniform circles.
- Don’t overfill, 1 rounded tablespoon of filling per cookie is perfect.
- After getting your filling ball, gently pat it into a disk and then add it on top of your crumble for easier spreading, before adding the cookie to the top.
Baking Tips:
- Look for dark golden edges on the crumble as your doneness indicator.
- Don’t skip the cooling time! The structure develops as it cools.
- Use parchment paper, not a silicone mat. You want good heat transfer to crisp up that crumble.
Flavor Variations:
- Add 1/2 teaspoon bourbon or rum to the pecan filling for an adult twist
- Mix chopped chocolate chips into the filling for chocolate pecan pie cookies
- Add a pinch of nutmeg or cardamom to the crumble for extra warmth
- Try a caramel drizzle instead of caramel or white chocolate
Why Toast the Pecans?
Toasting the pecans before adding them to the filling is optional but highly recommended. Here’s why it makes a difference:
- Deeper, nuttier flavor – Toasting brings out the natural oils and intensifies the pecan taste
- Better texture – Toasted pecans hold up better during baking and won’t get soggy
- Authentic pecan pie taste – Most traditional pecan pies use toasted pecans
The 3-5 minutes of toasting is absolutely worth it!
Troubleshooting
My filling is too oily:
- This can happen if the butter separates during cooking. Stir well once cooled, and if needed, gently blot excess oil from the surface with a paper towel before assembly.
- The filling will firm up significantly when chilled.
My cookies spread too much:
- Make sure your dough was properly chilled for the full fermentation time.
- Check that your oven temperature is accurate (use an oven thermometer).
- The dough should be cold when you cut and place the circles.
The filling leaked out:
- Make sure the filling was completely cold and thick before assembly.
- Don’t overfill, 1 rounded tablespoon is the right amount.
- Keep the filling away from the edges of the crumble layer.
The crumble got soggy:
- This can happen if there was excess oil in the filling.
- Make sure to cool completely on the pan before moving.
I can’t see the marble effect:
- Leave more gaps in the crumble layer when spreading it initially.
- Make sure you’re using enough filling (1 rounded tablespoon).
- The contrast develops as they bake and cool.
Frequently Asked Questions
Can I make these without a sourdough starter?
While the sourdough adds incredible flavor and texture, you can make these without a starter. For the cookie dough, replace the 120g sourdough starter with 60g all-purpose flour + 60g buttermilk (or regular milk) and increase the baking powder to 3/4 teaspoon. For the crumble, replace the 30g sourdough starter with 15g flour + 15g milk. However, you won’t get the fermentation benefits.
How long does the fermentation take?
Minimum 8 hours, but you can go up to 24-36 hours. Longer fermentation = more complex flavor. This makes it perfect for fitting into your schedule.
Can I freeze these cookies?
Yes! Freeze the baked, cooled cookies (without drizzle) in an airtight container for up to 2 months. Thaw at room temperature and add drizzle before serving.
Can I freeze the dough?
Absolutely! After the fermentation period, you can freeze the dough and crumble separately for up to 2 months. Thaw in the fridge overnight before assembly. Make the pecan filling fresh on baking day.
Do I have to use a food processor for the crumble?
No, the hand method works great too! The food processor just makes it faster and more uniform.
Why is my cookie dough hard to roll out?
If the dough is too cold and firm from the fridge, let it sit at room temperature for 10-15 minutes to soften slightly. If it’s fighting you, wrap it and chill it for 15-30 minutes to relax the gluten.
Can I make these smaller or larger?
Yes! Adjust the cutter size and the amount of filling/crumble accordingly. Smaller cookies (2”) may need less baking time; larger cookies (4”) may need more.
Nutrition Information (Per Cookie)
Approximate values for 1 cookie (recipe makes 12-15 cookies):
- Calories: 380-420
- Total Fat: 22-25g
- Saturated Fat: 10-12g
- Cholesterol: 65-75mg
- Sodium: 180-220mg
- Total Carbohydrates: 42-46g
- Dietary Fiber: 2-3g
- Sugars: 24-28g
- Protein: 5-6g
Note: Nutritional values are estimates and will vary based on exact measurements and ingredients used. Values include optional drizzle.
More Upside Down Cookie Recipes You’ll Love
If you enjoyed these pecan pie sourdough cookies, you’ll want to check out the rest of my upside down cookie series:
- S’more Sourdough Cookies – Graham cracker crumble, marshmallow filling, and chocolate chips
- Peach Pie Sourdough Cookies – Spiced peach filling with a buttery crumble
- Blueberry Pie Sourdough Cookies – Fresh blueberry filling with lemon zest
- Apple Pie Sourdough Cookies – Spiced apple filling with an brown sugar crumble
- Strawberry Shortcake Sourdough Cookies – Fresh strawberry compote with vanilla crumble
- Cherry Pie Sourdough Cookies – flavorful cherry filling with a brown sugar crumble
Each one uses the same upside-down baking method to create that stunning marbled effect!
The Final Word on Pecan Pie Sourdough Cookies
These pecan pie sourdough cookies are everything you love about pecan pie in cookie form, rich, buttery, nutty, and absolutely stunning to look at. The upside-down baking method creates a marbled masterpiece that’s impressive enough for holiday cookie exchanges but easy enough for weekend baking.
The long fermentation might sound intimidating, but it’s mostly hands-off time that fits beautifully into your schedule. Mix the dough and crumble on Day 1, let them ferment overnight, then assemble and bake on Day 2. The result is a cookie with complex flavor, incredible texture, and a wow-factor presentation.
Whether you’re a pecan pie fanatic, a sourdough enthusiast, or just someone who loves a unique cookie recipe, these pecan pie sourdough cookies deserve a spot in your baking repertoire.
Happy baking!
Did you make these pecan pie sourdough cookies? I’d love to see them! Tag me on Instagram or leave a comment below with your results!
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