Name: Sourdough Carrot Cake Whoopie Pies
Prep time: 20 min
Cook time: 10 min
Total time: 60 min
Ingredients: 3 cups all-purpose flour; 1 1/4 cups quick oats; 3/4 tsp baking soda; 1/2 tsp baking powder; 1 1/2 tsp ground cinnamon; 1/4 tsp ground ginger; 1/8 tsp ground nutmeg; 1/2 tsp salt; 1/2 cup unsalted butter, softened; 1/2 cup packed brown sugar; 1/3 cup granulated sugar; 1 large egg; 1 tsp vanilla extract; 1/2 cup sourdough starter or discard; 2 cups finely shredded carrot; 1 cup unsalted butter, softened; 2 cups powdered sugar; 1 jar marshmallow fluff; 1 tsp vanilla extract; 1/2 tsp ground cinnamon

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Sourdough carrot cake whoopie pies combine everything I love about soft carrot cake cookies with the classic charm of homemade whoopie pies. Made with sourdough starter, fresh shredded carrots, quick oats, and warm fall spices, these carrot cake whoopie pies are soft and moist inside while sturdy enough to sandwich with a creamy cinnamon filling. If you’ve been looking for a cozy recipe for whoopie pies or a delicious way to use your sourdough starter this fall, these sourdough whoopie pies are the perfect treat to bake!

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Soft, spiced carrot cake, sourdough starter, and a creamy cinnamon filling all tucked into one handheld fall treat—these sourdough carrot cake whoopie pies might be one of my favorite ways to use up starter this season. They’re packed with fresh shredded carrots and warm cinnamon, ginger, and nutmeg, giving them everything I love about carrot cake in a fun little sandwich. And since I always have sourdough starter around, turning those classic fall flavors into whoopie pies just made sense.

And these took a little experimenting!

My first test batch spread completely flat in the oven. I had nice little scooped mounds going into the oven, and then suddenly I had one giant sheet of carrot cake cookie. Not exactly the carrot cake whoopie pies I had pictured! My teenage sons looked so sad as they were expecting delicious whoopie pies to come out of that oven! However, I did not give up hope!

After adjusting the flour and oats, though, I finally got exactly what I wanted: a soft, moist little cake-cookie that holds its shape well enough to sandwich around a generous layer of cinnamon whoopie pie filling.

These aren’t quite traditional carrot cake cookies, and they aren’t little carrot cakes either. They’re right in the middle—and that’s exactly where I wanted them.

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What Are Sourdough Carrot Cake Whoopie Pies?

If you’ve never made sourdough whoopie pies before, think of them as two soft, cake-like cookies sandwiched around a fluffy filling. Traditional whoopie pies are often chocolate, but there are so many ways to change the flavors with the seasons. I do have the classic Amish Chocolate Whoopie Pies recipe straight from Lancaster, Ohio Amish Country if you are interested!

How to Make Amish Whoopie Pies!

For this fall version, I took the idea of a classic recipe for whoopie pies and gave it a carrot cake twist!

These sourdough carrot cake whoopie pies are made with fresh shredded carrots, sourdough starter, quick oats, brown sugar, and plenty of warm spices. The oats give them a little more structure and texture, while the carrots and sourdough starter keep the centers wonderfully moist.

Then there’s the filling.

I’m using a variation of my classic Amish whoopie pie filling, but adding cinnamon to make it perfect for fall. It’s creamy, sweet, fluffy, and just spiced enough to complement the carrot cake without covering up its flavor.

Why I Had to Adjust This Recipe

I want to talk about this because if you look at the ingredient list and think, Three cups of flour and 1¼ cups of oats?, there’s a reason!

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When I first started working on these carrot cake whoopie pies, the batter looked promising. It was thick enough to scoop into mounds and didn’t immediately spread on the baking sheet.

Then I baked my test batch.

They spread out completely flat!

The problem is that we’re putting quite a bit of moisture into these sourdough whoopie pies. There are 2 full cups of freshly shredded carrots plus ½ cup of sourdough starter. Carrots release additional moisture as they bake, so the dough needed more structure than I initially expected.

I added more flour and quick oats and tested them again. That was the difference. They finally held that thick, rounded carrot cake cookie shape I needed for a proper whoopie pie.

So don’t be alarmed when you see how thick this dough becomes. That’s intentional since it is a sourdough recipe.

The Texture We’re Going For

The easiest way I can describe these is:

Soft cookie + carrot cake = whoopie pie.

I didn’t want regular carrot cake cookies that were thin or chewy like traditional cookies. But I also didn’t want little pieces of fluffy carrot cake that would crumble apart as soon as I picked up the sandwich.

A good recipe for whoopie pies needs enough structure that you can actually hold the finished dessert.

These are soft and moist inside with a slightly chewy, cake-like texture, while the outside is sturdy enough to hold all that cinnamon filling.

They’re especially good once the filling has had a chance to settle between the two halves.

Why Sourdough Starter Works So Well in Whoopie Pies

I’m always looking for another way to use my sourdough starter besides making bread, and desserts are one of my favorite options.

The ½ cup of starter in these sourdough carrot cake whoopie pies contributes moisture and a little of that characteristic sourdough flavor without making the finished dessert taste sour.

Instead, it works beautifully with the brown sugar and warm spices.

You can use active starter or discard in this recipe for whoopie pies, which also makes it a handy recipe when you have discard that needs to be used.

Between the sourdough starter and fresh carrots, these sourdough whoopie pies stay wonderfully soft inside.

Ingredients for Sourdough Carrot Cake Whoopie Pies

You don’t need anything particularly unusual for these. Most of the ingredients are simple baking staples, along with fresh carrots and your sourdough starter.

For the Sourdough Carrot Cake Whoopie Pies

3 cups all-purpose flour
1¼ cups quick oats
¾ teaspoon baking soda
½ teaspoon baking powder
1½ teaspoons ground cinnamon
¼ teaspoon ground ginger
⅛ teaspoon ground nutmeg
½ teaspoon salt
½ cup unsalted butter, softened
½ cup packed brown sugar
⅓ cup granulated sugar
1 large egg
1 teaspoon vanilla extract
½ cup sourdough starter or discard
2 cups finely shredded carrots

For the Cinnamon Whoopie Pie Filling

1 cup unsalted butter, softened
2 cups powdered sugar
1 jar marshmallow fluff
1 teaspoon vanilla extract
½ teaspoon ground cinnamon

The cinnamon is the little fall adjustment I’m making to my classic whoopie pie filling. It ties the filling into all those warm spices in the carrot cake whoopie pies without making it overwhelmingly spicy.

How to Make Sourdough Carrot Cake Whoopie Pies

Making these sourdough carrot cake whoopie pies isn’t difficult, but there are a few things that really matter—especially the consistency of the dough and chilling it before baking.

Step 1: Cream the Butter and Sugars

Add the softened butter, brown sugar, and granulated sugar to a large mixing bowl.

Cream everything together until well combined and fluffy.

The brown sugar is especially nice in these carrot cake cookies because it adds moisture and a deeper flavor that works so well with the carrots and spices.

Step 2: Add the Wet Ingredients

Beat in the egg and vanilla extract.

Next, mix in the ½ cup of sourdough starter or discard until everything is thoroughly combined.

Don’t worry if the mixture doesn’t look exactly like traditional cookie dough at this point. We’re still adding quite a bit of flour, oats, and carrots.

Step 3: Combine the Dry Ingredients

In a separate bowl, combine:

Flour
Quick oats
Baking soda
Baking powder
Cinnamon
Ginger
Nutmeg
Salt

Mix the dry ingredients well so the spices and leavening are evenly distributed throughout your sourdough whoopie pies.

Step 4: Bring the Dough Together

Gradually add the dry mixture to the wet ingredients.

Once combined, fold in the 2 cups of finely shredded carrots.

Now take a look at your dough.

It should be very thick and scoopable.

It may look somewhere between extremely thick cake batter and very soft cookie dough. That’s what you want. A scoop of dough should sit in a mound rather than immediately flowing outward.

Remember my first batch! If these carrot cake whoopie pies don’t have enough structure, all that moisture from the carrots and starter can encourage them to spread.

Step 5: Chill the Dough

Cover the dough and refrigerate it for 20 to 30 minutes.

This gives the flour and oats a little time to absorb moisture while the butter firms back up.

Meanwhile, preheat your oven to 375°F.

Step 6: Scoop the Whoopie Pies

Line a cool baking sheet with parchment paper.

Scoop approximately 2 tablespoons of cold dough for each whoopie pie half.

Leave the dough in rounded mounds. Don’t flatten them like regular carrot cake cookies.

Remember that every finished whoopie pie requires two halves, so try to keep your scoops fairly consistent in size. That makes matching them up much easier later.

Step 7: Bake

Bake the sourdough carrot cake whoopie pies at 375°F for approximately 8 to 11 minutes.

I bake in a toaster oven that can run a little harsher than a full-sized oven, so I start checking mine early.

You’re not looking for hard or crispy cookies.

The tops should look set, the pies should have maintained their shape, and the centers should gently spring back when touched.

That’s when they’re ready.

Step 8: Let Them Cool

Allow the baked halves to sit on the baking sheet for approximately 10 minutes before transferring them to a cooling rack.

Let them cool completely before filling them.

Don’t rush this part. If you add butter-based filling to warm sourdough whoopie pies, you’ll end up with a melty mess. Ask me how I know!

Make the Cinnamon Whoopie Pie Filling

For these carrot cake whoopie pies, I’m using the classic filling from my Amish whoopie pie recipe with one simple fall adjustment: cinnamon.

Beat the softened butter until creamy.

Gradually add the powdered sugar and continue beating until smooth and fluffy. Add the marshmallow fluff and vanilla extract and beat until everything is thoroughly combined.

Finally, mix in ½ teaspoon of ground cinnamon.

That little bit of cinnamon turns my classic filling into a warm, creamy cinnamon filling that tastes wonderful against the spiced carrot cake cookies.

You can taste it at this point and see what you think. I like the cinnamon to complement the carrot cake rather than completely take over the filling.

Assemble the Carrot Cake Whoopie Pies

Once all your whoopie pie halves are completely cool, match them into pairs that are approximately the same size.

Turn one half upside down and add a generous amount of cinnamon filling to the flat side.

Place the second half on top and gently press until the filling reaches toward the edges.

And that’s it—you’ve made sourdough carrot cake whoopie pies!

Try not to press too hard. These are sturdy enough to hold the filling, but they’re still supposed to remain tender and cake-like.

How Many Whoopie Pies Does This Recipe Make?

My batch made about 15 large whoopie pies using approximately 2 tablespoons of dough for each half.

Remember that you’ll need two baked halves for every finished whoopie pie.

If you want smaller sourdough whoopie pies, you can reduce the amount of dough you scoop. Smaller ones will bake more quickly, though, so begin checking them earlier.

For me, the larger size is just right. They feel like a proper bakery-style fall dessert, and there’s plenty of room for that cinnamon filling in the middle.

Tips for the Best Carrot Cake Whoopie Pies

There are a few things I learned while developing this recipe for whoopie pies that can help you get the same soft-but-sturdy texture.

Finely shred your carrots. Smaller shreds distribute more evenly through the dough and make the finished whoopie pies easier to eat.
Don’t skip the chilling time. Give that thick dough 20 to 30 minutes in the refrigerator before baking.
Don’t flatten the scoops. Leave them in mounds so they bake into thicker halves.
Use a cool baking sheet. Don’t put cold dough onto a baking sheet that’s still hot from the previous batch.
Watch them closely. You want soft carrot cake cookies, not crispy ones.
Cool completely before filling. This is especially important with a butter-based filling.
Match similar-sized halves. Your finished sandwiches will look much nicer.

Most importantly, don’t keep baking them because they still feel soft. They will continue setting as they cool.

Can I Use Sourdough Discard?

Yes! This is one of the reasons I love making sourdough whoopie pies.

You can use sourdough discard or active starter in this recipe. You don’t need the starter to provide the primary leavening because we’re also using baking soda and baking powder.

That makes these sourdough carrot cake whoopie pies another delicious way to use up starter when you don’t necessarily need another loaf of bread.

And I don’t know about you, but turning extra sourdough starter into a fall dessert filled with cinnamon cream sounds pretty good to me!

Can I Make Smaller Carrot Cake Whoopie Pies?

Absolutely.

My carrot cake whoopie pies were fairly large, and I got about 15 finished sandwiches from the recipe.

For smaller ones, simply scoop less dough for each half. Just keep every scoop as consistent as possible so you can easily pair the baked carrot cake cookies together.

You’ll also want to reduce the baking time slightly and start checking them early.

How to Store Sourdough Whoopie Pies

Once filled, I recommend storing these sourdough whoopie pies in an airtight container.

You can place parchment paper between layers if you need to stack them. Since the filling contains butter and marshmallow fluff, I prefer keeping the assembled whoopie pies refrigerated for longer storage.

Let a refrigerated whoopie pie sit out briefly before eating if you prefer the cake and filling a little softer.

You can also individually wrap the carrot cake whoopie pies, which makes them convenient for grabbing one at a time without exposing the rest of the batch to air.

A Cozy Sourdough Dessert for Fall

I love recipes that come out of experimenting in my own kitchen, and these sourdough carrot cake whoopie pies definitely earned their place in my fall baking rotation.

The first batch spreading flat could have been the end of this experiment, but I’m glad I kept working with it. Adding enough flour and oats gave me exactly the structure I needed without losing that soft, moist carrot cake center.

The finished carrot cake whoopie pies have fresh carrots, sourdough starter, oats, brown sugar, cinnamon, ginger, and nutmeg packed into those soft little cakes, with creamy cinnamon filling sandwiched right in the middle.

They’re not quite cake.

They’re not quite carrot cake cookies.

They’re sourdough whoopie pies—and that’s exactly what I wanted.

If you’ve been searching for a cozy fall recipe for whoopie pies and have sourdough starter waiting on your counter, this is a delicious way to put it to work!

Sourdough Carrot Cake Whoopie Pies

These sourdough carrot cake whoopie pies are soft, moist, and warmly spiced with cinnamon, ginger, and nutmeg. Fresh shredded carrots, quick oats, and sourdough starter create tender, cake-like cookies that are sturdy enough to sandwich with a creamy cinnamon filling for a cozy homemade fall treat.

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Prep Time 20

Cook Time 10

Chill Time 30

Total Time 1