These sourdough morning glory muffins make the most of shredded carrots, apple, and seeds, for a delicious breakfast muffin that uses up some of your sourdough discard. The starter adds just a touch of tang that's wonderfully balanced by the sweet carrot, apple, and dried fruit. This recipe is dairy and nut-free.

Here's a comprehensive list of all of our sourdough discard recipes if you find you always have too much discard on hand. If you like these muffins, you'll probably love our sourdough blueberry muffins, too!

Morning glory muffins on plates, halved with butter on the side.
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Ingredient Notes and Substitutions

  • Raisins: golden raisins have a nice plump sweetness, but any raisins will work! Try dried cranberries or another dried berry for a bit of a twist.
  • Seeds: we made these muffins nut-free for school snacks. Use any combination of seeds or nuts you like - we love hazelnuts, pecans, and walnuts.
  • Sugar: if you like a sweeter muffin, double the sugar. You can also use raw, brown, or even coconut sugar here.
  • Flour: substitute half whole-wheat flour for a more wholesome muffin that still has a nice light texture. You can use all wholegrain flour but note that the muffins will be denser in that case.


Morning glory muffins steps 1 to 4, mixing dry and wet ingredients and mixed batter.

Step 1: in a large bowl whisk together the flour, cinnamon, baking powder, baking soda, and salt.

Step 2: add the grated carrots and apple, coconut, raisins, and seeds to the flour mixture and stir to coat.

Step 3: in another bowl, whisk together the wet ingredients.

Step 4: add the wet ingredients to the dry and fold together.

Apple carrot muffins before and after baking.

Step 5: spoon the muffin mixture evenly into lined muffin cups.

Step 6: bake until golden and cool before serving.

Top Tips

  • Use any starter: this recipe uses discard from sourdough starter. If you use the levain method, don't worry! You can use active starter, too, but be sure to weigh everything to be accurate.
  • Follow the order: adding the carrots, apple, and other add-ins to the flour and stirring together before adding the wet ingredients prevents over-mixing, which can lead to a less tender muffin. Feel free to stir dry into wet and then add carrots, etc. if you prefer.
  • Use a food processor: grate carrots and apples coarsely with a standard box grater. To speed things up, you can use the grating attachment on a food processor.

Recipe Notes

This may seem like a lot of batter after mixing, but will make 12 muffins!

The muffins can be made in a standing mixer if you prefer, with the paddle attachment, but be careful not to over-mix.

For a stronger sourdough flavour and easier to digest muffins, keep the batter in the fridge for up to 12 hours before portioning out and baking.

Starting the oven at a higher temperature will make for fluffier muffins. Reducing the temperature halfway through ensures that the muffins will be baked through without burning on the outside.

How to Store

Storage: store the muffins in a sealed container on the counter for a couple days, or in the fridge for 5-7 days.

Freezing: freeze in an airtight container for up to three months. Thaw on the counter for an hour or so, or gently defrost in the microwave before you eat.


Is sourdough good for gut health?

Sourdough can be beneficial for gut health, because it contains good bacteria that can support a healthy digestive system. Many people find sourdough baked goods easier to digest.

Can you save sourdough discard to use later?

Yes! Keep your discard in the fridge for weeks and use for recipes like sourdough muffins, crackers, pancakes, and more.

Can you use 2 week old sourdough discard?

Definitely, if it's been stored in the fridge. Note that it might have a pretty strong sour flavour and will impart that to anything you're using it in.

If you make this Sourdough Muffin recipe or any other muffin recipes on the Baked Collective, please take a moment to rate the recipe and leave a comment below. It’s such a help to others who want to try the recipe. For more baking, follow along on Instagram, TikTok, and YouTube.

Morning glory muffins on plates, halved with butter on the side.
Print Recipe
5 from 4 votes

Sourdough Morning Glory Muffins

These sourdough morning glory muffins make the most of shredded carrots, apple, and seeds, for a delicious muffin made with sourdough discard.
Prep Time25 minutes
Cook Time20 minutes
Total Time45 minutes
Author: Kelly Neil
Yield: 12


  • Measuring cups and spoons or a digital kitchen scale
  • 12-cup muffin tin
  • muffin cups
  • Mixing bowl
  • Whisk
  • Rubber spatula or wooden spoon
  • Wire rack


Dry Ingredients

  • 1-½ cups all-purpose flour
  • 1 tablespoon cinnamon
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon salt


  • 2 cups carrots grated, approximately 2 medium carrots
  • 1 cup grated apple approximately 1 medium-small apple
  • ½ cup unsweetened shredded coconut
  • ½ cup raisins
  • ½ cup seeds and/or nuts we used a mix of sunflower, pumpkin, and flax seeds

Wet Ingredients

  • 1 cup sourdough starter
  • ¼ cup vegetable or other neutral-flavoured oil, plus 1 tablespoon for greasing the muffin tin
  • ¼ cup sugar
  • 2 eggs
  • 1 tablespoon vanilla extract
  • Extra coarse sugar for topping optional


  • Preheat the oven to 425ºF (220ºC).
  • Lightly grease a standard 12-cup muffin tin with oil then line the cups with paper muffin wrappers. Set aside.
  • In a large bowl, whisk together the flour, cinnamon, baking powder, baking soda, and salt.
  • Add the grated carrots and apple, coconut, raisins, and seeds to the flour mixture. Use a rubber spatula or wooden spoon to stir everything together, breaking up any larger clumps of grated carrot or apple as needed. 
  • In a second bowl, whisk together the sourdough starter, oil, sugar, eggs and vanilla until smooth.
  • Make a well in the carrot-flour mixture and pour in the wet ingredients. Again, using a rubber spatula or wooden spoon, fold everything together until just combined with a few streaks of flour remaining. 
  • Divide the muffin batter evenly between the cups in the prepared muffin tin. Top the muffins with a little coarse sugar if you'd like.
  • Place the tin in the preheated oven and bake the muffins for 10 minutes.
  • Reduce the heat to 375ºF (190ºC) and continue to bake the muffins for 10 minutes more.
  • Remove the muffins from the oven, placing the tin on a wire rack to cool for 10 to 15 minutes.
  • Transfer the muffins from the tin to the wire rack and let them cool completely before storing them an airtight container or zip-top plastic bag.


Serving: 1muffin | Calories: 169kcal | Carbohydrates: 16g | Protein: 4g | Fat: 11g | Saturated Fat: 3g | Polyunsaturated Fat: 7g | Cholesterol: 31mg | Sodium: 372mg | Fiber: 2g | Sugar: 7g


  1. 5 stars
    I have made this recipe several times now and it is my absolute favorite muffin recipe now. I love finding more ways to use my sourdough discard and that this recipe doesn’t have a ton of sugar and oil. I use 1 cup spelt flour and 1/2 cup rolled oats in place of the all purpose flour and add 1/2 cup unsweetened applesauce since using whole grain requires more liquid and melted coconut oil instead of the vegetable oil and it turns out great!

  2. 5 stars
    These are delicious! I made just a few substitutions: did half whole wheat flour and half all purpose, threw in less than a 1/4 cup of mini chocolate chips, and used a cup of applesauce instead of shredding an apple. Also added chia seeds and dried dates instead of raisins. Will definitely be making these again!

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