The Best Sourdough Carrot Cupcakes Recipe with Cream Cheese Frosting

These sourdough carrot cupcakes are a fresh take on the traditional. They combine sweet, spiced carrots with a slightly tangy, soft texture from the sourdough starter. They’re topped with a smooth, rich cream cheese icing that makes them even better.

They’re perfect for any event, from a family get-together to just a comforting snack at home. Plus, they freeze well, so you can have a delicious bite ready anytime.

Whether you’re into sourdough or looking for a new take on carrot cake, I think these cupcakes could quickly become a favorite. If you love baking with sourdough, you might also enjoy exploring these Easter sourdough recipes for more inspiration and delicious ideas.

Sourdough Carrot Cupcakes

Using discard sourdough starter, these carrot cupcakes are sweet and moist, topped with a delicious and simple cream cheese frosting.  No sourdough taste!
Prep Time 30 minutes
Cook Time 25 minutes
Total Time 55 minutes
Serving Size 26 cupcakes

Equipment

  • 12-cup Cupcake pans
  • Cupcake liners
  • Mixer (stand mixer or hand mixer)
  • Large mixing bowl
  • Wire rack

Ingredients 

Carrot Cake

  • 1 ½ cup vegetable oil
  • 2 cups white sugar
  • 1 cup sourdough starter (discard/ unfed)
  • 3 eggs
  • 1 cup canned crushed pineapple (drained, about 8 oz)
  • 2 cups carrots (grated, about 4 medium carrots)
  • ½ cup golden raisins
  • 2 teaspoons vanilla
  • 2 ½ cups all purpose flour
  • 2 teaspoons cinnamon
  • ¼ teaspoon allspice
  • ½ teaspoon salt
  • 1 teaspoon baking soda

Cream Cheese Frosting

  • 8 ounces cream cheese (room temperature)
  • 12 ounces butter (melted)
  • 4 cups powdered sugar
  • pinch salt (if using unsalted butter)
  • 3 teaspoons vanilla
  • 2 tablespoons milk or cream (if icing is too thick)

Instructions 

For the Cupcakes:

  • Preheat the oven. Preheat the oven to 350°F (175°C) and line the muffin pans with cupcake liners. This recipe yields 24 very full cupcakes or 26 smaller ones.
  • Mix the wet ingredients. Combine the vegetable oil and white sugar in a large mixing bowl. Then, beat well until fully combined and creamy. Next, add the sourdough starter discard and gently mix it into the batter. Add the eggs one at a time, beating well after each addition. Stir in the vanilla extract.
  • Add the carrots, pineapple, and raisins. Reduce your mixer speed to low and gently fold in the grated carrots, drained pineapple, and golden raisins until evenly distributed throughout the batter.
  • Prepare the dry ingredients. In a separate large bowl, whisk together the flour, cinnamon, allspice, salt, and baking soda. Gradually add the dry ingredients to the wet ingredients, mixing gently after each addition until just combined. Be careful not to overmix.
  • Fill and bake. Divide the batter evenly among the prepared cupcake liners. Bake in the preheated oven for 25 minutes, or until a cake tester inserted into the center of a cupcake comes out clean and the tops are lightly bouncy when pressed.
  • Cool the cupcakes. Allow the cupcakes to cool in the pan for a few minutes before transferring them to a wire rack to cool completely before frosting.

For the Cream Cheese Frosting:

  • Beat the cream cheese and butter. Using a stand or hand mixer, beat the room temperature cream cheese and melted butter on medium speed until smooth and creamy. It may appear lumpy at first, but continue beating until fully combined.
  • Add the vanilla and salt. Mix in the vanilla extract. If you're using unsalted butter, add a pinch of salt. Otherwise, skip the salt.
  • Add the powdered sugar. Gradually add the powdered sugar, one cup at a time, starting on low speed to prevent a sugar cloud, then increasing the speed until the frosting is smooth and creamy.
  • Adjust the consistency. If the frosting is too thick, add milk or cream, one teaspoon at a time, until the desired consistency is reached. If it becomes too thin, refrigerate the frosting for 30 minutes before using.
  • Frost the cupcakes: Once the cupcakes are completely cooled, generously frost them using a piping bag or a spatula.

Video

Notes

Shred the carrots finely before adding them to the batter for a smoother texture and to make sure the cupcakes stay moist.  Avoid store-bought shredded carrots, as they’re usually too coarse and can dry out.
Squeeze as much liquid as possible from the crushed pineapple before adding it.  Too much liquid can ruin the batter’s consistency, making your cupcakes less appealing.
To make sure everything mixes well, let your eggs, cream cheese, and butter warm up to room temperature before you start.  This trick helps everything blend more easily for a smooth batter and creamy frosting.
If your cream cheese frosting is too runny, chilling it in the refrigerator for about 15 minutes should help it stiffen.  A little milk or cream can thin it out if it’s too stiff.
Want to make a cake instead?  Mix evenly into two 8-inch cake pans and bake for about 45 minutes, checking with a cake tester to make sure it’s done.
This recipe has plenty of cream cheese frosting, so if you like less frosting on your cake or cupcakes, you might want to make half the amount suggested.
Feel free to customize the recipe by adding crushed walnuts, shredded coconut, or even leaving out the raisins.  Just remember to reduce the vegetable oil to 1 1/4 cups to balance the added moisture from these ingredients.
If you’re looking for something a bit more special, this same mixture can be used to make a layered carrot cake.  For a little extra touch, try topping your cupcakes with crushed nuts or a sprinkle of coconut.
Calories: 364kcal | Carbohydrates: 52g | Protein: 3g | Fat: 17g | Saturated Fat: 12g | Cholesterol: 30mg | Sodium: 144mg | Potassium: 102mg | Fiber: 1g | Sugar: 39g | Vitamin A: 1811IU | Vitamin C: 1mg | Calcium: 35mg | Iron: 1mg

More Tips:

Before you start, make sure to line your cupcake pans properly to make sure easy removal. If you’re looking for tips, here’s the best way to line cupcake pans to get it just right.

Baking soda is crucial in making these cupcakes rise and giving them the right texture. Check that your baking soda hasn’t been lying around for over six months, as old baking soda might not do its job well, making your cupcakes come out heavier.

When you measure flour, fill your measuring cup with a spoon and then level it off with a knife’s flat edge. If you scoop directly from the flour bag, you might pack too much flour into the cup, drying your cupcakes.

After you mix the dry and wet ingredients, stir just enough to combine them. Mixing too much could make your cupcakes heavy instead of light and airy.

Fill your cupcake liners to about ⅔ full. Filling them too much can make the cupcakes overflow and sink, while insufficient batter leads to smaller, less satisfying cupcakes. Consider adding a creamy surprise inside your cupcakes for an extra indulgent twist. This Vanilla Cream Filling pairs perfectly with the carrot cake and cream cheese frosting flavors.

Cupcakes can be baked differently in different ovens. Start checking if they’re done a bit before the recommended time. When they’re cooked just right, a toothpick should come out clean or with a few moist crumbs on it.

Use a piping bag with a star tip to create a professional-looking finish on your frosting. It looks good and helps you get an even layer of frosting on each cupcake.

Though it’s tempting to frost them while they’re still warm, wait until your cupcakes have cooled down completely. Frosting them too soon can cause the frosting to melt and make a mess. Cool them on a wire rack before you add the cream cheese frosting.

While this rich cream cheese frosting is a classic topping, you might also want to try adding a surprise inside. Check out these cupcake-filling recipes for some delicious ideas.

sourdough carrot cupcake with cream cheese frosting resting on on towel

Serving Suggestions

Serve these cupcakes with hot spiced tea, fresh fruit salad, creamy vanilla ice cream, roasted pecans, or lemon-infused water.

Key Ingredients and Tools

To whip up these cupcakes, you’ll need a handful of important tools and ingredients that make the recipe shine. Here’s a list of what you’ll need:

sourdough carrot cupcake with bite taken out
  • Leftover Sourdough Starter: This is the part of the sourdough starter you haven’t refreshed with new flour and water. It brings a unique tangy taste to your cupcakes. Some bakeries or online communities might offer sourdough starter if you need it quickly. If you’re out of sourdough starter, yogurt or buttermilk can be used as a substitute, but the flavor will differ.
  • Vegetable oil: It’s widely used in baking to keep cupcakes moist. Melted coconut oil or butter can be used as a substitute, but this might slightly change the texture.
  • Golden Raisins: They add a delicious sweetness and texture. They are usually found in the dried fruit section of the grocery store, but they can sometimes be less common than regular raisins. If you can’t get hold of golden raisins, regular raisins or dried cranberries are good alternatives.
  • Canned Crushed Pineapple: This adds both moisture and a hint of sweetness. Just make sure it’s well-drained so the batter doesn’t get too soggy. Unsweetened applesauce can be a good stand-in to keep the batter moist.
  • Fine Grater: This tool is super helpful for grating the carrots finely enough to mix them into the batter perfectly. You can pick one up in the kitchen section of most stores.
  • Stand or Hand Mixer: You’ll need one of these to get your frosting smooth. A stand mixer is great for ease, particularly for blending the cream cheese and butter, but a hand mixer works well, too.
  • Cupcake Liners: These prevent the cupcakes from sticking to the pan and make cleaning up a breeze. Look for them in the baking section of the store, near where all the cake mix and other baking stuff are kept.

Having these things ready will set you up for cupcake success.

Troubleshooting and Help

Can I use a fed sourdough starter instead of discard?

Absolutely! You can use a fed, active starter if that’s what you have. Just remember that it might give the cupcakes a slightly more pronounced sourdough flavor, which could be a nice twist!

Can I substitute whole wheat flour for the all-purpose flour?

You can, but remember that whole wheat flour will make the cupcakes denser and may give them a slightly nutty flavor. If you want to try it, I’d suggest using half whole wheat and half all-purpose flour to keep the texture nice and light.

What if I don’t have a fine grater for the carrots?

No worries! If you don’t have a fine grater, you can use a regular box grater on the smaller side. The texture might be a bit chunkier, but it’ll still work. Make sure to grate the carrots as finely as possible so they blend well into the batter.

Can I skip the golden raisins if I don’t like them?

Of course! If you’re not a fan of golden raisins, feel free to leave them out or replace them with something you like, such as chopped nuts, dried cranberries, or even a handful of shredded coconut.

My cupcakes didn’t rise much—what went wrong?

Oh no! That can happen if your baking soda is old or if the batter was overmixed. Make sure your baking soda is fresh (less than six months old), and when mixing the batter, stir just until the ingredients are combined. Overmixing can knock out the air and make the cupcakes dense.

My cream cheese frosting turned out too soft—what can I do?

Oh no! That happens sometimes, especially if the butter was too warm when you started. Just stir the frosting in the fridge for about 15-20 minutes to let it firm up, then stir it before frosting the cupcakes.

What should I do if I don’t have a stand mixer?

No problem! You can use a hand mixer or mix by hand if you’re up for a little arm workout. The key is to make sure everything is well combined, especially when making the frosting, so take your time and mix until smooth.

Can I make these cupcakes ahead of time?

Definitely! If the cupcakes are unfrosted, you can bake them a day or two ahead and store them in an airtight container at room temperature. If you’ve already frosted them, keep them in the fridge. They also freeze really well, so you can bake and freeze them for up to a month—just thaw at room temperature before serving.

What if I don’t like cream cheese frosting?

No problem at all! If cream cheese frosting isn’t your thing, you can try a simple buttercream, a tangy lemon glaze, or even just dust the tops with powdered sugar for a lighter option. Whatever you like better!

Storage Instructions

If your cupcakes don’t have frosting, keep them in a sealed container at room temperature. They’ll stay fresh for about two days. This method helps keep them moist if you plan to add frosting later.

For cupcakes with frosting, place them in a sealed container in the fridge. They’ll be good for up to 5 days. Just let them warm up for about 20-30 minutes before you eat them so they’re not too cold.

To freeze cupcakes without frosting, wrap each in cling film and put them in a freezer bag or sealed container. They’ll last in the freezer for up to one month. Thaw them at room temperature for a few hours before you frost and eat them.

You can also freeze cupcakes with frosting, but the frosting texture might change once thawed. First, freeze the frosted cupcakes on a tray in the freezer until the frosting is hard. Next, wrap each in cling film and store in a freezer-friendly container for up to 1 month. Thaw them in the fridge overnight or at room temperature for a few hours before serving.

Keep these tips in mind to enjoy your cupcakes at their best!

I hope these Sourdough Carrot Cupcakes bring something special to your baking routine. They’re a simple and delicious way to use your sourdough discard, creating a treat everyone will love. The blend of sweet carrots, tangy sourdough, and rich cream cheese frosting makes these cupcakes a delicious indulgence you’ll want to make again and again.

Whether for a special occasion or just because I’m sure they’ll become a favorite in your home. Enjoy them year-round, whether sharing with friends or savoring one with a cup of tea.

If you want to try more unique cupcake flavors, these Coconut Cupcakes with Lemon Curd offer a bright and tangy twist that’s perfect for any occasion.

carrot cupcakes on wooden bread board with plates nearby
picture of smiling female

By Katie Shaw

Katie lives in Virginia with her husband, three daughters, a chocolate lab, and over thirty chickens. She loves creating simple tutorials for sourdough, bread, and soap. Her recipes, articles, and YouTube videos reach millions of people per year.

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Recipe Rating




35 Comments

  1. 5 stars
    I made this as a cake and used a buttermilk glaze instead of cream cheese frosting. The cake is moist, delicious and a great use of my unfed starter!

  2. 5 stars
    So so so yummy. I substituted a mix of half vegetable shortening and half butter, and used1 cup sourdough starter instead of half. Put the nuts raisins coconut and walnuts as well. For the icing I used vanilla bean paste and only three cups sugar. I just cannot seem to follow a recipe, but it ended up making 24 cupcakes and a 9X9 pan of cake.

  3. 5 stars
    5 Stars! I didn’t have canned pineapple on hand, so subbed with unsweetened apple sauce. Only made half the amount of frosting (based on the icing sugar I had in my cupboard) and that was the perfect amount (although I could easily eat the frosting by the spoonful). Thanks for sharing this lovely recipe!!

  4. 5 stars
    DELICIOUS!
    I only used 1 cup of sugar and left them unfrosted – I was looking for carrot muffin recipe when I stumbled upon this one. SO good – a definite keeper!

  5. 5 stars
    Because of health issues, I had to go dairy and gluten free. This has been a hard transition for me AND my family. Finding a recipe that tastes just as good as we were accustomed to is difficult, to say the least. I made these cupcakes for Easter with a GF flour mix. They turned out so good! The cakes were moist, decadent and delicious. Even my dad requested to take some home with him. (That was such a compliment to me!) The recipe makes quite a few cupcakes so you can freeze some for later. A few weeks after Easter, my parents came over for dinner. Dad was so happy when I pulled out a few cupcakes and heated them up. Definitely a keeper!

  6. I made these with my cup for cup gluten free flour and they turned out too oily and crumbly , sorry don’t know if I could only use normal flour and also normal sour dough starter . Please help as was not very nice turn out

  7. My kiddos are sensitive to pineapples. Would you have any suggestions to replace this item? Is it necessary? This recipe sounds and looks delicious

    1. I would just leave it out. you could try applesauce but I think it might make the batter too wet. they’ll be fine without the pineapple 🙂

    2. 4 stars
      We used canned peach instead and it turned out great. Also subbed all butter/oils with coconut oil, icing was way too much for us so definitely would make half in the future.

  8. THESE WERE AWESOME!! My family loves them too! I made these yesterday, and now there are only 6 left! This recipe made 24 cupcakes and 4 small ramikin cakes. Love the addition of raisins and pineapple. It made these almost healthy!! And the frosting recipe makes A LOT of frosting. I had to freeze half of it to use later!

  9. This recipe looks fantastic, but 12 oz of butter seems to be a LOT of butter for the frosting.

  10. 5 stars
    I’m not a huge carrot cake fan, but I tried this recipe because I had lots of carrots and lots of sourdough. I used gluten free sourdough and flour, and applesauce instead of pineapple. They turned out moist and light, not too sweet, and the spice was perfect. These are not just the best carrot cake cupcakes I’ve ever had, these are the best CUPCAKES I’ve ever had. ???? I’ve shared the recipe with quite a few friends already, but my family wasn’t interested in sharing the cupcakes with friends.

  11. Oh my goodness!! This sounds absolutely delicious!!! I love sourdough, carrot cake, and cream cheese frosting! Great baking tips as well!

    1. This is such perfect timing! I started a new sourdough starter today and was thinking that I should start looking up some good recipes to utilize the “discarded” portions!