Sourdough Apple Carrot Muffins (Overnight Long Fermented Recipe!)
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These long-fermented sourdough apple carrot muffins are packed with freshly grated carrots and honeycrisp apples, sweetened with honey, and just the right amount of cinnamon for a nutritious and delicious breakfast option! Simply combine the milk, flour, and active sourdough starter at night, cover it, let it ferment while you sleep, and then bake the muffins in the morning!
It’s not often you see something here that is healthy (what can I say? I love me a good dessert!)- but these muffins are healthy, scrumptious, and long fermented, so you have all the gut-healthy benefits of naturally leavened sourdough.
They are also incredibly moist. The texture is light, fluffy, and just a *hint* of sweet. You also get to control the amount of sweet you’d like these muffins to contain, because you can add anywhere from 1/2 cup to 1 full cup of honey. I, of course, used a full cup.
Looking for more sourdough recipes? Check these out:
The best part about these muffins is how hands-off they are. The night before you plan to bake them, you will mix together the milk, flour, and active, bubbly sourdough starter. Then you will cover it and let it sit at room temperature for 8-12 hours.
When you wake in the morning, it will have formed a dough that has risen due to the fermentation. That’s perfect. You’ll add in the carrots, apples, and the rest of the wet ingredients, and then mix until everything is combined.
I recommend an electric mixer for this because the dough is not like regular muffin batter. You’ll need to really mix the fermented dough with the rest of the ingredients!
Alright, let’s dig into it!
Why You’ll Love These Muffins
- They’re simple. Wholesome ingredients, not fancy “bakery-style” crumb topping. These muffins are simple, easy to make, and delicious without all the frill that some muffin recipes require.
- They’re nutritious. You’ll get some veggies in your kids first thing in the morning! My kiddos absolutely love these muffins and you’ll feel good knowing you’re giving them a fermented sourdough muffin with veggies and fruit.
- They’re hands-off. Very little work is needed to make these muffins.
Why Long Ferment?
Long fermentation allows the sourdough starter to slowly break down the flour overnight, which can make baked goods easier to digest and gentler on the gut. This process helps reduce phytic acid in the grains, making nutrients more available and flavors more developed.
In these muffins, the long ferment also creates a soft, tender crumb, adds subtle depth without a strong sour flavor, and pairs beautifully with warm spices, honey, apple, and carrot. The result is a muffin that feels both nourishing and cozy—perfect for everyday baking.
Ingredients For Carrot Apple Sourdough Muffins
Overnight Ferment
- All-purpose flour – I use unbleached, organic flour. Bread flour also works.
- Active sourdough starter – make sure your sourdough starter is fed, bubbly, and ready to ferment! Alternatively, you can use sourdough discard and make the muffins the same day without fermenting overnight.
- Whole milk – I prefer whole milk. Other dairy milks also work. I use cold milk to slow down the fermentation process since it is overnight.
Muffin Batter
- Apple, shredded – one medium apple–I prefer honeycrisp, but use what you’ve got! I don’t peel my apple, but you certainly can.
- Carrot, shredded – one large carrot. I do not peel mine, but you certainly can.
- Butter, melted – I use salted butter–unsalted butter also works, just add an additional 1/4 teaspoon of salt.
- Honey – You can also sub in sugar, but I prefer honey for my “healthier” muffin options.
- Eggs
- Full-fat Greek yogurt – Full-fat whole milk Greek yogurt is the best here. Sour cream also works!
- Vanilla extract
- Ground cinnamon
- Baking powder
- Baking soda
- Salt
Step-By-Step Instructions
In a large mixing bowl, combine the flour, active sourdough starter, and milk. Mix until smooth and fully combined. Cover and let rest at room temperature for 8–12 hours.
The next morning, preheat the oven to 425°F (220°C). Line two muffin tins with muffin liners and set aside.
Shred the apple and carrot, then gently pat dry with a paper towel to remove excess moisture.
Use your hands to mix in the shredded apple and carrot until combined throughout.
In a separate bowl, whisk together the melted butter, honey, eggs, Greek yogurt, vanilla extract, and cinnamon until smooth.
Pour the wet mixture into the bowl with the fermented dough. Using an electric hand mixer or stand mixer, mix until fully combined. The batter will be thick at first, but will come together as you mix.
Sprinkle the baking powder, baking soda, and salt over the batter. Mix just until incorporated.
Divide the batter evenly between the prepared muffin liners, filling each nearly to the top.
Bake at 425°F (220°C) for 10 minutes, then—without opening the oven door—reduce the oven temperature to 350°F (175°C) and bake for an additional 10 minutes, or until the muffins are set and a toothpick inserted into the center comes out clean.
Remove from the oven and allow muffins to cool in the pan for 5–10 minutes before transferring to a wire rack.
Equipment Needed
- Large mixing bowl
- Medium mixing bowl
- Electric hand mixer or stand mixer
- Whisk
- Box grater or food grater
- Measuring cups and spoons
- Rubber spatula
- Muffin tins
- Muffin liners
- Baking sheets
- Paper towels
- Wire cooling rack
Storage
- Room Temperature: Store cooled muffins in an airtight container at room temperature for up to 2 days.
- Freezer: Once completely cooled, freeze muffins in a freezer-safe bag or container for up to 3 months. Thaw at room temperature or warm gently before serving.
Looking for more sourdough breakfast recipes? Try these!
Sourdough Apple Carrot Muffins (Overnight Long-Fermented Recipe!)
Ingredients
Overnight Ferment
- 2 cups all-purpose flour 240 grams
- 1/2 cup active sourdough starter 120 grams
- 1 cup whole milk cold milk, 240 grams
Muffin Batter
- 1 medium apple shredded and patted dry, 130 grams
- 1 large carrot shredded and patted dry, 100 grams
- 1/2 cup butter melted, 113 grams
- 1 cup honey 340 grams
- 2 large eggs
- 1/2 cup full-fat Greek yogurt 120 grams
- 1 teaspoon vanilla extract 5 grams
- 2 teaspoons ground cinnamon 5 grams
- 2 teaspoons baking powder 8 grams
- 1 teaspoon baking soda 5 grams
- 1/4 teaspoon salt
Instructions
The Night Before
- In a large mixing bowl, combine the flour, active sourdough starter, and whole milk.
- Mix until fully combined and no dry flour remains.
- Cover the bowl and let the mixture rest at room temperature for 8–12 hours.
The Next Morning
- Preheat the oven to 425°F.
- Line two muffin tins with muffin liners and set aside.
- Shred the apple and carrot, then gently pat dry with a paper towel to remove excess moisture.
- Add the shredded apple and carrot to the fermented dough.
- In a separate bowl, whisk together the melted butter, honey, eggs, Greek yogurt, vanilla extract, and cinnamon.
- Pour the wet ingredients into the fermented dough.
- Using an electric hand mixer or stand mixer, mix until fully combined. The batter will be thick at first but will come together smoothly.
- Mix in the baking powder, baking soda, and salt until just incorporated.
- Divide the batter evenly among the prepared muffin liners.
- Bake at 425°F for 10 minutes, then—without opening the oven door—reduce the oven temperature to 350°F.
- Continue baking for an additional 10 minutes, or until the muffins are set and a toothpick inserted into the center comes out clean.
- Remove from the oven and allow to cool slightly before serving.
Notes
- Room Temperature: Store cooled muffins in an airtight container at room temperature for up to 2 days.
- Freezer: Once completely cooled, freeze muffins in a freezer-safe bag or container for up to 3 months. Thaw at room temperature or warm gently before serving.
