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Sourdough Discard Muffins

Whole Wheat Apple Carrot Muffins with Sourdough Discard

Moist, rich, and bursting with flavor—the perfect baking recipe for apple season. Enjoy these sourdough apple carrot muffins for breakfast, a snack, or dessert.

Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes
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Recipe Index | Ferment | Sourdough Discard | Sourdough Discard Muffins

Whole Wheat Apple Carrot Muffins with Sourdough Discard

Moist, rich, and bursting with flavor—the perfect baking recipe for apple season. Enjoy these sourdough apple carrot muffins for breakfast, a snack, or dessert.

Whole Wheat Apple Carrot Muffins

If you love baking with sourdough starter and are looking for a creative way to use your sourdough discard during apple season this fall, we have a delightful treat for you—Whole Wheat Apple Carrot Muffins with Sourdough Discard!

These muffins are packed with fresh, crisp apples, sweet grated carrots, and warm cinnamon, creating a nutritious and delicious snack that’s perfect anytime.

Whole Wheat Apple Carrot Muffins with Sourdough Discard

Sourdough is a beloved ingredient in bread-making and offers numerous health benefits. The fermentation process used to create sourdough bread enhances its nutritional profile, making it easier to digest than traditional yeast bread. In sourdough, lactic acid bacteria break down gluten, fructans, and phytic acid, which can benefit individuals with gluten or FODMAP sensitivities.

While muffins are not usually long-fermented, they can be! Though I don’t long ferment these apple carrot muffins, some readers have told me they’ve had success fermenting the batter overnight in the fridge for improved digestibility. Feel free to try fermenting the muffin batter overnight in the refrigerator before preheating your oven and filling your muffin tin with batter.

Don’t Over-Mix These Apple Carrot Muffins

One crucial tip when making these apple carrot muffins is to avoid overmixing the batter. Overmixing can result in dense muffins, primarily due to gluten formation, rather than the light and fluffy texture we want.

Gluten, a protein present in flour, gives structure to baked goods. However, excessive mixing develops gluten strands, leading to a denser texture. To prevent this, gently mix the dry and wet ingredients until combined, ensuring there are still some lumps and streaks of flour in the batter.

This technique raises the muffins correctly, resulting in a tender crumb. Another helpful tip is to use a thin aluminum muffin tin with paper liners. For even baking, a metal muffin tin works much better than a silicone muffin pan.

Hands use a knife to chop apples for the apple carrot muffin recipe.
The dry ingredient mixture is in a bowl for apple carrot muffins.

Why Are My Apple Carrot Muffins Dry?

Dry muffins can result from several factors related to ingredients and baking techniques. Here are some common reasons and tips to help you troubleshoot:

  1. Too Much Flour: Adding too much flour can make muffins dry. For accuracy, measure your flour correctly using the spoon-and-level method.
  2. Overmixing: Overmixing the batter can cause too much gluten to develop, making the muffins dense and dry. Mix until just combined to avoid this.
  3. Baking Time: Baking muffins for too long can cause them to dry out. Check them a few minutes before the recipe’s suggested time by inserting a toothpick; it should come out clean but not dry.
  4. Moisture Balance: The combination of apples and carrots helps retain moisture. If your muffins are dry, use enough fresh, juicy apples and carrots to achieve the right balance.
  5. Low-Fat Content: If your recipe uses low-fat ingredients or substitutes, the muffins may lack moisture. My recipe calls for butter, which helps keep the muffins from drying.
The wet ingredient mixture for apple carrot muffins in a white bowl.
The wet and dry ingredients are mixed into a bowl to make the apple carrot muffins batter.

What is the Secret to Moist Muffins?

Adding fruit and vegetables to muffins is the secret to achieving a moist and tender texture that keeps these baked treats irresistibly soft.

Fruits like apples and vegetables like carrots naturally contain high water content, which releases moisture as the muffins bake. This moisture infusion prevents the muffins from drying out and enhances their softness. Moreover, fruits contribute to the flavor profile, adding a fresh, natural sweetness that complements the other ingredients.

The natural sugars in apples caramelize during baking, creating pockets of juicy, flavorful bites within the muffin. The pectin in apples is a natural thickener, contributing to the moist, luscious crumb. Incorporating fruit and vegetables elevates the taste and ensures that each muffin is tender and moist.

Hands use a spoon to fill a muffin tin with batter.

Storing Sourdough Apple Muffins

Properly storing baked apple carrot muffins ensures they remain fresh and delicious. Here are some tips on how to store them effectively:

  • Room Temperature Storage:
    • Allow the muffins to cool completely.
    • Place them in an airtight container lined with paper towels to absorb excess moisture.
    • Store at room temperature for up to 3-4 days.
  • Refrigeration:
    • If the weather is hot or humid, consider refrigerating the muffins.
    • Wrap each muffin individually in plastic wrap to prevent drying out.
    • Store in an airtight container in the fridge for up to one week.
  • Freezing Muffins:
    • Cool the muffins completely before freezing.
    • Place wrapped muffins in a freezer-safe bag or container.
    • Label it with the date and freeze it for up to 3 months.
  • Reheating Frozen Muffins:
    • Remove the desired number of muffins from the freezer.
    • Microwave on high for 20-30 seconds or until warm.
    • Alternatively, preheat the oven to 350°F (175°C) and heat the muffins for 10-15 minutes until warmed.

Following these tips, your Whole Wheat Apple Carrot Muffins with Sourdough Discard will stay deliciously fresh, ready for breakfast, snacks, or whenever you need a healthy, satisfying treat!

More Muffin Recipes

  • Low-Sugar Blueberry Protein Muffins with Sourdough Discard
  • Zucchini Blueberry Muffins with Sourdough Discard
  • Double Chocolate Cherry Muffins with Sourdough Discard
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Sourdough Discard Muffins

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5 from 1 review

Whole Wheat Apple Carrot Muffins with Sourdough Discard

A festive fall snack that uses up some sourdough discard? Sign us up! Moist, rich, and bursting with flavor—the perfect baking recipe for fall and apple season. Enjoy these sourdough apple carrot muffins for breakfast, a snack, or dessert.

  • Prep: 10 minutes
  • Cook: 30 minutes
  • Total Time: 40 minutes

Ingredients

  • 1 cup whole wheat flour
  • 1 1/4 cups all purpose flour
  • 1/2 cup brown sugar, packed
  • 1/2 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1 teaspoon salt
  • 1 teaspoon cinnamon
  • 1 cup apples, chopped
  • 1 cup shredded carrots
  • 1/2 cup grass-fed butter, room temperature soft/melted
  • 1/2 cup sourdough starter, room temperature
  • 2 teaspoons vanilla extract
  • 1/2 cup whole milk, room temperature
  • 2 eggs, room temperature

Icing Drizzle

  • 1/3 cup powdered sugar
  • 2–3 teaspoons whole milk

Instructions

  • Preheat your oven to 350° F.
  • Line a muffin tin with paper liners.
  • Chop/mince the apples and carrots.
  • In a medium-large mixing bowl, combine the flour, sugar, cinnamon, baking soda, baking powder, salt, apples and carrots.
  • In a separate bowl, combine the butter, sourdough starter, vanilla, whole milk, and two eggs. Whisk until combined.
  • Gently fold the wet ingredients into the dry ingredients until everything is just combined. Do not over-mix. The batter should be thick, and it’s okay if there are clumps.
  • Spoon the batter into the muffin tins.
  • Bake for about 30 minutes total. Rotate the pan halfway through.
  • Allow to cool completely.
  • Optional—add icing: Add the milk 1 teaspoon at a time to the powdered sugar, keeping the icing super thick but able to be drizzled.

Did you make this recipe?

Please leave a 5-star review below if you loved it! Tag @cultured.guru on Instagram

 

Nutrition information is auto-calculated and estimated as close as possible. We are not responsible for any errors. We have tested the recipe for accuracy, but your results may vary.

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Kaitlynn Fenley Author, Educator, Food Microbiologist
Kaitlynn is a food microbiologist and fermentation expert teaching people how to ferment foods and drinks at home.
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  1. Audrey
    01|18|2024

    These are the best muffins! Made them and was blown away by texture and flavor! (Didn’t have potato starch so simply omitted)

    Reply
    1. Kaitlynn Fenley
      01|22|2024

      Thank you for leaving a review! I’m glad they turned out great without the starch too.

      Reply

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Fermentation is a gift from the microbes of this e Fermentation is a gift from the microbes of this earth.

When we had a food business, I could never shake the feeling that fermentation is not meant to be sold to you from a fluorescently lit grocery shelf in an endless cycle of waste. Fermentation is meant to be cultivated in your home, with your hands, with intention and love in a sustainable, grateful practice of reciprocity and nourishment. 

This is the story of how we got here. 

After so many lessons learned, our small fermentation business is now value aligned, peaceful, fulfilling, and happy.  It often seems like the gut feelings (the microbes within us) guided us in the right direction. To teach. 

You can learn for free on our blog, or you can enroll in our online courses (we extended our new year sale!) Either way, with me as your teacher, you’ll learn to adopt a holistic perspective on the microbial ecosystems that influence our food, lives, and the planet.
My favorite topic I teach in our online course is My favorite topic I teach in our online course is called Fermentation Variables. The whole lesson is centered around the fact that there are six main variables that influence the outcome of fermentation.

Here they are, in no particular order:

Sugar
Salt
Oxygen
Acidity
Temperature
Time

Temperature and time depend on each other most closely. 

that means, for all of our foods and drinks that ferment at room temp, things slow way down in the winter cold. 

The fermentation timeline is simply longer when it’s colder (and faster when it’s hotter). The microbes, kind of like us, make things happen slowly in the cold winter. 

I think this is yet another sign from nature that we’re supposed to rest and be gentle and gracious with deadlines, work, and not rush things this time of year. 

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Touching cabbage and dough is just as good as “touching grass” lol 

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#fermentation
Yes cooking kills the microbes, but idc. I mean, I Yes cooking kills the microbes, but idc. I mean, I care, but in a “thank you for your service microbes” kinda way. 🫡

Cider braised pork and sauerkraut is a perfect choice for New Year’s or any winter meal! I lovvveee pairing it with butternut squash polenta bc it’s full of vitamin C for cold and flu szn. 

Eating pork and sauerkraut on New Year’s Day is a tradition. And I really do think it brings good luck and prosperity.

Get the recipe on our blog, linked in my profile and in story highlights! 

I’m really looking forward to creating more recipes like this in the new year, to show you all the joys of incorporating ferments into meals and recipes 😌✨ stay tuned! 

#newyear #sauerkraut #fermentation
One Christmas I gifted everyone in my family the N One Christmas I gifted everyone in my family the New York style sourdough bagels and they were thrilled. (The bagels we’re actually way under proofed, but I still gifted them and everyone loved them lol)

You can get the full recipe on my blog! And these can be made with discard and instant yeast or with just active starter.

 All the details are in the 5-star rated recipe on my website. 

#bagels #sourdough
This cookie dough is long-fermented overnight in t This cookie dough is long-fermented overnight in the fridge for the softest, most flavorful, melt-in your mouth sourdough gingerbread cookies.

For Christmas 2025, I tried something new with these cookies. I created a gingerbread sourdough starter to use in this recipe! I made it by feeding some of my established starter a mix that includes molasses and gingerbread spices. I just added the instructions for the gingerbread starter in the notes of my cookie recipe.

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My gingerbread sourdough starter recipe 🎄✨ Like a My gingerbread sourdough starter recipe 🎄✨

Like and save for some fun Christmas sourdough baking! 

I made this up a few days ago to use in my soft sourdough gingerbread cookies. (cookie recipe is in my recipe index on my website!)

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