These sourdough carrot muffins are naturally sweetened and have a fluffy spiced cake paired with a cream cheese filling, and topped with oat streusel. It’s a delightful combination for any time of year.

sourdough carrot muffin cut in half on a cutting board with more muffins in the background

The air is starting to feel chilly, pumpkins and apples have begun lining the tables, and the last of the summer vegetables are being pulled from the garden.

Carrots are one of my favorite things to grow, being that they are so simple. Just spread the tiny seeds, water, thin out a bit, and be surprised every time you pull them out of the ground.

An easy-growing root vegetable that yields big results. So, what do you do with your carrot harvest?ย 

You can roast them, ferment them, put them in soup, or bake them into a muffin. Hiding veggies in a muffin is an amazing way to get the pickiest of eaters to eat their veggies. 

Add in some cream cheese filling and sprinkle with streusel topping, and you’ll find they wonโ€™t mind one bit.

These muffins are a delicious combination of hearty and sweet flavors without any refined sugar. Nothing hits the spot quite like a warm muffin straight from the oven.

sourdough carrot muffin on wood cutting board with a napkin and candle stick in the background

Easy Recipe With Sourdough Starter

This recipe can be whipped up in a pinch, or long fermented to get the healthful benefits of fermented grain. Just one reason we love sourdough so much here on the farm.

Use discard or active sourdough starter. Either will work.

If you are new to sourdough recipes, make sure to check out how to make a sourdough starter here and how to care for one.

3 sourdough carrot muffins on a wood cutting board

A Few Tips On Making Sourdough Muffins

  • You can choose to do either the streusel topping or the cream cheese center, or both, or neither one.
  • Add a 1โ„4 cup of raisins or nuts, if you desire.
  • Bake the muffins in the upper third of the oven for a better rise.
  • Make sure not to over-mix the muffin batter. Muffins will be dense and tough if you mix the batter too much. Just stir with a spoon until the ingredients are just combined.
  • Let the batter rest in the fridge for at least an hour if you have time, as this will really help in getting domed muffin tops.

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Tools you may need:

Muffin tin

Measuring cups and spoons

Large bowl

Stand mixer (for long fermented version).

Nutrimill (optional)

Box grater

a sourdough carrot cake muffins cut in half on a wood cutting board with more muffins in the background

How To Make Sourdough Carrot Muffins

Preheat the oven to 425 degrees. 

Grease muffin tin well, or line with paper liners.

In a medium bowl, whisk together the spelt flour, salt, baking powder, baking soda, and spices.ย 

In a separate large bowl, whisk together melted coconut oil and coconut sugar, then incorporate one room-temperature egg at a time.ย 

Next, stir in sourdough starter, crushed pineapple, and grated carrot. No need to drain any water off the carrot. You want the extra moisture in these muffins.

Gradually add dry ingredients to the wet ingredients and mix until just combined. If you have time, allow mixture to sit in the fridge for one hour, as this will give the muffins a better rise.

For the cream cheese filling:

Vigorously whip together softened cream cheese with maple syrup in a small bowl until itโ€™s light and fluffy.

Make The Streusel Topping

In a separate small bowl, combine oats, spelt flour, coconut sugar, cinnamon, and salt. Mix well.

Incorporate cold butter until small pieces are evenly distributed in the mixture.

Put Carrot Muffins Together And Bake

Distribute half the muffin batter into the prepared muffin wells. Evenly distribute the cream cheese mixture across the 12 muffin tins, then cover with the remaining half of the muffin batter. 

Top with the streusel mixture. 

Bake in a preheated oven at 425 for 5-6 minutes, and then drop the oven temperature to 350 (no need to open the oven door) and continue to bake for 13-15 minutes (total bake time is around 20 minutes).

Test muffins with a cake tester. Allow to cool.

oat streusel on top of sourdough carrot cake muffin on a wood cutting board

Long Fermented Sourdough Carrot Muffins Version:

Mix together flour, sugar, sourdough starter, and melted coconut oil. Cover and allow to ferment for 8-24 hours.ย 

The next day, add shredded carrots, salt, leaveners, spices, and other remaining ingredients. Mix until just combined (I recommend using a stand mixer). Bake as directed the next day.

Storage

Place in an airtight container in the fridge for up to a week, or freeze for up to three months.

Find More Desserts Straight From The Farmhouse:

If you try this recipe and love it, I would love if you gave it 5 stars! Thank you! Tag me on Instagram @farmhouseonboone

Sourdough Carrot Muffins

4.59 from 41 votes
Sourdough carrot muffins have a delicious, cream cheese filling and a coconut sugar streusel topping.
Prep: 10 minutes
Cook: 20 minutes
Additional Time: 8 hours
Total: 8 hours 30 minutes
Servings: 12
3 sourdough carrot muffins on a wood cutting board
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Ingredients 

  • 1 1/2 cups spelt flour, can also use all purpose or freshly milled wheat
  • 1/4 teaspoon salt
  • 1 1/2 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons cinnamon
  • 1/4 teaspoon nutmeg
  • 1/2 teaspoon ginger

Wet Ingredients:

  • 1/3 cup melted coconut oil
  • 3/4 cup coconut sugar
  • 2 large eggs
  • 1 1/2 cups grated carrot, 150g
  • 1/2 cup sourdough starter
  • 1/4 cup crushed pineapple

Cream Cheese Filling:

  • 4 oz softened cream cheese
  • 2 tablespoons maple syrup

Streusel Topping:

  • 1/4 cup oats
  • 1/2 cup spelt flour
  • 1/4 cup coconut sugar
  • 1/2 teaspoon cinnamon
  • Pinch salt
  • 4 tablespoons cold butter

Instructions 

  • Preheat the oven to 425 degrees.
  • Grease muffin tin wells or line with paper liners.
  • In a medium bowl, whisk together the spelt flour, salt, baking powder, baking soda and spices.
  • In a separate large bowl, whisk together melted coconut oil and coconut sugar, then incorporate one room temperature egg at a time.
  • Next, stir in sourdough starter, crushed pineapple, and grated carrot.
  • Gradually add dry ingredients to the wet ingredients and mix until just combined.
  • Optional- Allow the mixture to sit in the fridge for one hour.
  • Vigorously whip together softened cream cheese with maple syrup in a small bowl until itโ€™s light and fluffy.
  • In a separate small bowl, combine oats, spelt flour, coconut sugar, cinnamon, and salt. Mix well.
  • Incorporate cold butter until small pieces of butter are evenly distributed in the mixture.
  • Distribute half the muffin batter into the prepared muffin wells.
  • Evenly distribute the cream cheese mixture across the 12 muffin tins, then cover with the remaining half of the muffin batter.
  • Top with the streusel mixture.
  • Bake in a preheated oven at 425 for 5-6 minutes, and then drop the oven temperature to 350 and continue to bake for 13-15 minutes.
  • Test muffins with a cake tester. Allow to cool.

Notes

  • You can choose to do either the streusel topping or the cream cheese center, both or neither one.
  • If you really like nuts and raisins in your carrot cake, add 1โ„4 cup for more texture.
  • Make sure not to over-mix the muffin batter. Muffins will be dense and tough if you mix the batter too much. Just stir with a spoon until the ingredients are just combined.
  • For a better rise, let the batter rest in the fridge for at least an hour.

Nutrition

Calories: 288kcal | Carbohydrates: 35g | Protein: 5g | Fat: 15g | Saturated Fat: 10g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.2g | Cholesterol: 51mg | Sodium: 303mg | Potassium: 98mg | Fiber: 4g | Sugar: 13g | Vitamin A: 2965IU | Vitamin C: 1mg | Calcium: 58mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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4.59 from 41 votes (40 ratings without comment)

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49 Comments

  1. KB says:

    5 stars
    Amazing muffins!!! Sooo sooo good!
    Thank you for the recipe.
    I had a question, do you think I can make these into cookies? Would the same temperature work and the same amount of flour?

    Thank you!

    1. Lisa Bass says:

      I don’t think you could make these into cookies without altering the recipe quite a bit.

  2. Jenny says:

    Hi! How do we store the muffins? Room temp or refrigerator?

    1. Lisa Bass says:

      Room temperature works great!

  3. Gosia says:

    Is there anything else I can use other than pineapple? I have all ingredients but not pineapple

    1. Lisa Bass says:

      I’ve not personally tried it without the pineapple.

  4. Kim says:

    Hi Lisa
    Why do you add baking powder and baking soda to the muffins. I always thought that with sourdough there was no need for these two ingredients. Excuse my ignorance but have to ask to know. Love your website and recipes. You are amazing!

    1. Lisa Bass says:

      Quick recipes require the baking powder because they don’t have enough time to build their own yeast and rise on their own.

  5. Rossella says:

    Can I use discard with this as well? Or does it have to be active starter?

    1. Lisa Bass says:

      Discard will definitely work.