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Experience apple pie in handheld cookie form with these irresistible apple pie sourdough cookies! These easy apple pie cookies feature a fermented sourdough cookie base that develops complex flavors through 8-24 hour cold fermentation, creating the perfect vessel for homemade apple pie filling. The unique upside-down assembly method layers spiced crumble on the bottom, warm apple pie cookie filling in the middle, and sourdough cookie dough on top, sealing everything together for a mess-free treat.

Once baked and flipped, you get beautiful apple pie cookies with crumble topping finished with a rich caramel drizzle. Each bite delivers all the flavors of classic apple pie in a perfectly portable, stackable cookie that’s ideal for fall baking, holiday cookie exchanges, or whenever you’re craving apple pie dessert without the fuss of making a whole pie.

If you love this concept, make sure to check out my Cherry Pie Sourdough Cookies, Blueberry Pie Sourdough Cookies, and S’mores Upside Down Sourdough Cookies for the full upside-down cookie series.

Table of Contents

• Why You Will Love These Cookies
• What Is Sourdough Cookie Dough?
• Ingredients
• Best Apples for Apple Pie Cookies
• How to Make Apple Pie Sourdough Cookies
• How to make caramel in the microwave
• Tips for Perfect Results
• Storage and Make-Ahead Instructions
• Frequently Asked Questions
• Recipe Card

Why You Will Love These Cookies

This recipe has become one of my favorite things to make in the fall, and once you try it I think you will understand why. Here is what makes it special:

• All the flavor of apple pie with none of the pie-making fuss
• The cold-fermented dough develops a deep, complex buttery flavor that a standard cookie dough simply cannot match
• The upside-down method creates a naturally beautiful crumble top with zero decorating required
• Homemade apple filling with real spices, not a can
• Homemade caramel drizzle that takes about 10 minutes and is completely worth it
• Perfect for fall baking, holiday cookie exchanges, and Thanksgiving dessert tables
• Make the dough and crumble the night before for a low-stress bake day

What Is Sourdough Cookie Dough?

Sourdough cookie dough uses active sourdough starter in place of or in addition to traditional leaveners. The starter adds subtle complexity to the flavor, helps with texture, and makes the dough ferment-friendly so it can sit in the fridge overnight without any issues.

You do not need any experience with sourdough bread to make these cookies. If you have a starter that passes the float test, you are ready to go. The dough comes together like any other cookie dough, it just gets an 8 to 24 hour rest in the refrigerator before baking, which is actually a great thing for your schedule.

The fermentation window is flexible. Eight hours gives you good flavor. Twenty-four hours gives you even better flavor. Both work perfectly.

Ingredients

Here is everything you need, broken into the four components of this recipe. Full measurements with gram weights and cup conversions are in the recipe card below.

Sourdough Cookie Base

Active sourdough starter, unsalted butter, powdered sugar, brown sugar, egg, vanilla extract, almond extract (optional), all-purpose flour, baking powder, salt, and cream of tartar.

Apple Pie Spiced Crumble

All-purpose flour, brown sugar, active sourdough starter, cold butter, salt, vanilla extract, powdered sugar, cinnamon, nutmeg, and ground ginger.

Homemade Apple Pie Filling

Granny Smith, Honeycrisp apples or my favorite Keepsake, brown sugar, cornstarch, fresh lemon juice, vanilla extract, ground cinnamon, nutmeg, ground ginger, salt, and butter.

Caramel Drizzle

Granulated sugar, water, heavy cream, unsalted butter, salt, and vanilla extract.

Best Apples for Apple Pie Cookies

Not all apples bake the same way, and it matters here because you want a filling that is saucy and jammy, not watery or mushy. Here is a breakdown of the best options:

Granny Smith is the classic choice. Tart, firm, and it holds its shape beautifully when cooked. If you want that sharp apple pie contrast against the sweet crumble and caramel, use Granny Smith.

Honeycrisp brings natural sweetness and a little more give. It breaks down slightly more than Granny Smith, which creates a jammier filling.

Keepsake is my personal favorite for this recipe. It is a cold-hardy Minnesota apple with a firm, dense flesh that holds up beautifully when cooked, meaning it will not turn to mush in the filling. The flavor is sweet with just enough tartness to keep it interesting, and it bakes into the most gorgeous, jammy filling without needing much added sugar to balance it out. If you can get your hands on Keepsake apples at a local orchard or farmers market this fall, use them here. You will not regret it.

Braeburn sits right in the middle. Sweet-tart balance with great texture for baking. Less common at the grocery store but worth grabbing when you see it.

Golden Delicious breaks down more than the others, giving you a softer, more cohesive filling. If you like your apple pie filling on the smoother side, this is your apple.

The best move is mixing two varieties. Half Granny Smith for structure and tartness, half Honeycrisp for sweetness and depth. The filling will have more complex flavor and better texture than using a single variety.

How to Make Apple Pie Sourdough Cookies

This recipe is a two-day process, but the active time on both days is minimal. Day one is about 15 minutes of hands-on work. Day two is about 30 minutes. The rest is fermentation, cooling, and setting time that happens on its own.

Day 1: Cookie Dough and Crumble

Make the Cookie Dough

In a large bowl, cream together softened butter, powdered sugar, and brown sugar until light and fluffy. Add the egg, vanilla extract, and almond extract if using, and mix well. Add the sourdough starter and mix until combined.

In a separate bowl, whisk together the flour, baking powder, salt, and cream of tartar. Gradually add the dry ingredients to the wet ingredients and mix until just combined.

Dump the dough onto plastic wrap, wrap tightly, and refrigerate for 8 to 24 hours.

Make the Fermented Crumble

Food Processor Method (preferred): Add flour, brown sugar, salt, powdered sugar, cinnamon, nutmeg, and ginger to the food processor. Pulse 3 to 4 times to combine. Add cold cubed butter and pulse 10 to 15 times in short bursts until the mixture resembles coarse crumbs. Add vanilla and sourdough starter and pulse 1 to 2 times just to incorporate. You want a sandy, clumping texture, not a dough ball. Squeeze a pinch together and it should hold its shape.

Hand Method: Combine all dry ingredients in a medium bowl. Add cold cubed butter and cut in with a pastry cutter or your fingers until the mixture resembles coarse crumbs. Add vanilla and mix gently.

Cover the crumble and refrigerate alongside the cookie dough for 8 to 24 hours.

Day 2: Assembly and Baking

Make the Apple Filling

In a medium saucepan, combine diced apples, brown sugar, lemon juice, vanilla, cinnamon, nutmeg, ginger, and salt. Add butter and cook over medium heat, stirring gently, for 5 to 8 minutes until the apples begin to soften and release their juices.

Whisk the cornstarch with 2 tablespoons of water in a small bowl to make a slurry. Add the slurry to the apple mixture and stir gently. Continue cooking for 3 to 5 more minutes until the filling thickens and the apples are tender but still hold their shape.

Remove from heat and cool completely, at least 45 minutes. Cover with plastic wrap and refrigerate for faster cooling. The filling must be fully cold before assembly.

Assemble the Cookies

Preheat oven to 350F. Line a large baking sheet with parchment paper.

Using a 2.5 to 3 inch circle cutter as a guide, spread about 2 rounded tablespoons of crumble onto the parchment in a loose circle. Do not pack it down. For a more rustic look with filling peeking through, leave some irregular gaps in the crumble.

Top each crumble circle with 1 to 1.5 rounded tablespoons of cooled apple filling. Keep it toward the center and away from the edges.

Roll the fermented cookie dough out on a lightly floured surface to a rough rectangle, about 12 by 9 inches, approximately 3/8 inch thick. Cut out circles using your cutter.

Place a cookie circle on top of each crumble and filling stack. Gently press down to seal the edges. Tuck any escaping crumbs underneath.

Tip: If the dough starts resisting, wrap it and refrigerate for 15 minutes to let the gluten relax before continuing.

Bake

Bake for 18 to 22 minutes, until you can see dark golden browning on the crumble edges around the bottom of each cookie.

Remove from oven and let cool completely on the baking sheet. This step is non-negotiable. The filling continues to set as the cookies cool. Once fully cooled, gently flip each cookie so the crumble side faces up.

Make the Caramel

In a heavy-bottomed saucepan, combine sugar and water over medium heat. Swirl the pan gently (do not stir with a spoon) until the sugar dissolves and the mixture begins to bubble. Keep swirling and cook without stirring for 8 to 12 minutes until the mixture turns deep amber.

Remove from heat and carefully whisk in the warmed heavy cream. It will bubble vigorously, this is normal. Add butter, salt, and vanilla and whisk until smooth. Cool for 5 to 10 minutes until slightly thickened but still pourable.

While the caramel is still warm, use a spoon or piping bag to drizzle it over the cooled cookies. Allow to set for 30 to 45 minutes before serving.

How to Make the Caramel Drizzle (Microwave Method)

I use a microwave caramel for this recipe and I am never going back to the stovetop. No candy thermometer, no standing over a hot pan nervously swirling, just smooth, rich caramel in under five minutes. Here is exactly how I do it.

Ingredients

67g granulated sugar (1/3 cup)
15g water (1 tablespoon)
30g heavy cream, warmed (2 tablespoons)
15g unsalted butter (1 tablespoon)
1g salt (pinch)
2.5g vanilla extract (1/2 teaspoon)

Instructions

Combine the sugar and water in a large microwave-safe bowl. The mixture will bubble up significantly, so make sure your bowl has plenty of room.

Microwave on high for 1 minute, then check. Continue microwaving in 30 second increments for another minute, checking the color each time. Once you start to see any color change at all, switch to 15 second increments and watch it closely. You are looking for a honey-gold color, not dark amber yet.

Pull it from the microwave as soon as it reaches that honey-gold stage and let it sit on the counter for 2 to 3 minutes. The carryover heat will continue to darken it to a deep amber while it rests. Do not skip this step.

While the caramel rests, warm your heavy cream and butter together until hot. Once the caramel has reached a deep amber color, slowly add the hot cream and butter one tablespoon at a time, stirring carefully. It will bubble up vigorously, this is completely normal.

Stir in the salt and vanilla until smooth. Let cool for 5 to 10 minutes until slightly thickened but still pourable, then drizzle over your cooled cookies.

Total microwave time will be approximately 2 to 2.5 minutes depending on your wattage. Every microwave is different, so watch the color closely rather than following the timing exactly. Sugar can go from perfect to burnt quickly, especially in smaller batches.

Tip: If your caramel cools and thickens before you are ready to drizzle, reheat it in the microwave in 10 second bursts until pourable again.

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Tips for Perfect Results

Apple prep matters. Dice apples into uniform 1/4 inch pieces so they cook evenly. Irregular sizes mean some pieces turn mushy while others are still firm.

Cold filling only. Hot or warm filling will soften the crumble and prevent the cookie from holding its shape after flipping. Refrigerate it if you are in a rush.

Dough thickness is key. Rolling to 3/8 inch ensures the cookie bakes through and has enough structure to hold the filling once flipped.

Do not rush the cooling. Removing cookies too early will cause the filling to slide and the cookie to fall apart. Give them the full cooling time on the pan before you touch them.

Use a flexible spatula. A thin, flexible spatula makes lifting the cookies off the parchment much easier. You can also peel the parchment away from underneath rather than lifting the cookie itself.

Dough resisting the cutter? Refrigerate your scraps for 15 minutes between rolls. Cold dough cuts cleanly and does not fight the cutter.

Crumble spacing tip. For more apple filling to show through the finished cookies, spread the crumble in an irregular circle with slight gaps throughout. This creates a rustic look and lets the spiced apple filling peek through the topping.

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Storage and Make-Ahead Instructions

Room temperature: Store cookies covered at room temperature for up to 2 days.

Refrigerator: Transfer to the refrigerator after day 2. They will keep for up to 5 days. Bring to room temperature before serving for best texture.

Freezer: Freeze baked cookies without caramel on a sheet pan until solid, then transfer to a freezer-safe bag for up to 2 months. Thaw overnight in the refrigerator and add fresh caramel drizzle before serving.

This recipe is genuinely ideal for making in stages. Here is the make-ahead timeline:

• Cookie dough: Make up to 3 days ahead, keep wrapped in the refrigerator
• Crumble: Make up to 3 days ahead, refrigerated
• Apple filling: Make up to 3 days ahead, covered in the refrigerator
• Caramel: Make up to 1 week ahead, reheat gently over low heat or in the microwave in 10 second bursts until pourable

Mix the dough and crumble on Thursday, make the filling on Friday, and bake on Saturday with minimal active effort.

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Frequently Asked Questions

Can I make these without sourdough starter?

I have not tested this myself, but if you need a substitute, sourdough starter is equal parts flour and water so you cannot simply swap it out for something else without adjusting the hydration. To replace the 120g of starter in the cookie base, try 60g of Greek yogurt and 60g of whole milk. For the crumble, replace the 30g of starter with 15g of Greek yogurt and 15g of whole milk. The yogurt brings fat, protein, and a little tang, and the milk brings the hydration back into balance across both components. The flavor will not be quite the same since you lose that fermented depth, but the dough and crumble structure should hold up. If you try it, I would love to hear how it goes!

Do these taste like sourdough bread?

Not at all. The sourdough starter adds a subtle buttery complexity to the base but there is no sour or yeasty flavor. Think of it as flavor insurance. It just makes everything taste more interesting.

My stove top caramel turned grainy. What happened?

Stirring is the most common cause. Once the sugar starts caramelizing, swirl the pan instead of stirring with a spoon. Stirring agitates the sugar crystals and causes them to seize up and turn grainy.

Can I use store-bought caramel?

Absolutely. A good quality store-bought caramel sauce works well if you want to simplify. Warm it until pourable before drizzling.

Can I use store-bought apple pie filling?

You can, but the homemade filling is worth the extra 15 minutes. Store-bought is often too wet and too sweet and not enough apples, which affects both the flavor balance and the texture of the finished cookie.

Why are my cookies falling apart when I flip them?

The most likely cause is flipping before the cookies are fully cooled. The filling needs time to set completely on the pan. Even if they feel firm on top, give them the full cooling time before flipping.

Can I make these smaller or larger?

Yes. Use a smaller cutter (about 2 inches) for bite-sized versions and reduce baking time by 3 to 4 minutes. For larger cookies, increase baking time and watch for the same golden crumble browning at the edges as your doneness cue.

How many cookies does this recipe make?

This recipe makes approximately 12 to 15 cookies depending on the size of your cutter.

If you make these apple pie sourdough cookies, I want to see them! Drop a comment below and tell me how they turned out, or tag me on Instagram at @h3artofthehome. And if you have not already, sign up for the newsletter so you never miss a new recipe.

Looking for more from the upside-down cookie series?

• Cherry Pie Sourdough Cookies
• Blueberry Pie Sourdough Cookies
• S’mores Upside Down Sourdough Cookies
• Apple Pie Sourdough Cookie Cups
• Strawberry Shortcake Cookies
• Pecan Pie Cookies

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Recipe Card

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