Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe (2024)

A batch of these Healthy Whole Wheat Morning Glory Sourdough Muffins is just what you need to fuel your morning or reboot your afternoon. They’re loaded with flavor, packed with nutrition, and best of all, made with sourdough starter!

Another day starts, and you know a healthy breakfast isn’t going to happen on its own. But that doesn’t mean you need to slave, half-awake, just to avoid the usual milk and cereal routine.

Imagine, instead, the scent of warm cinnamon and apple swirling in the air a measly half-hour after waking, letting you know breakfast is almost served.

And best of all? You didn’t have to do any work to make it happen because you whipped up these delicious whole-wheat Morning Glory Sourdough Muffins the night before.

Once those hand-held packages of fresh nourishment pop out of the oven, you’ll be set with a satisfying start to your day. See also: everything tastes better when it’s baked in a muffin pan.

Pair them with a smoothie or some eggs, then save the rest to go with your lunch or dinner. If you have any leftovers, that is.

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What Are Morning Glory Muffins?

Morning glory muffins are hearty little packages of shredded carrot and apple, some nuts or seeds, and occasionally dried fruit in a spiced whole-grain batter, baked to perfection.

Many recipes also call for raisins, but that’ll never happen here.

I was one of those poor children who was fooled by a raisin cookie.

You understand now, don’t you?

So while you won’t find raisins in my recipe, you’re welcome to add them to yours if you like them (and don’t have trust issues with cookies as I do now).

You’ll find a healthy serving of nutrition in these tasty morsels, too.

  • They’re packed with fiber thanks to the whole wheat, ground flax, apple, carrot, and pumpkin seeds. This supports healthy digestion and improved health overall.
  • Apple and carrot provide additional phytonutrients like Vitamin C, Vitamin A (specifically beta-carotene from the carrot), and multiple antioxidants.
  • Pumpkin seeds and ground flax seeds give you a boost of minerals and omega-3 fatty acids for additional health support.
Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe (2)

Most morning glory recipes usually call for much more sugar than you want when you’re trying to create nourishing, healthy food.

Thankfully, all that sugar really isn’t necessary. This recipe uses a moderate amount to give a slightly sweet flavor, but won’t overpower your taste buds (or pancreas) if you eat two or three.

Since this recipe is light on sugar and doesn’t contain extra oil, the muffins won’t have the super soft and moist texture of bakery and coffee shop muffins. We love them this way, though. They’re a bit rustic and just perfect for soaking up yummy pastured butter or tropical coconut oil.

If you want that typical soft and sweet muffin experience, you can try doubling the sugar and using heavy cream in place of the milk.

How to Make Muffins with Sourdough Starter

Sourdough starter is an amazing way to prepare any baked item, including muffins.

If you’re new to the world of sourdough, start here with my article How to Make, Store, and Care for a Sourdough Starter for simple instructions.

With sourdough, you can mix up your muffins the night before, let them rise while you sleep, and simply bake in the morning for a stress-free breakfast.

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Aside from being so convenient, sourdough starter offers health benefits by making the wheat easier to digest and making the nutrients more bioavailable.

Not to mention the incredible flavor sourdough gives everything!

You might worry about letting a sourdough batter rise overnight when it contains eggs, and that’s a fair concern.

You can let your batter rise in the refrigerator for 24 hours if you’re not comfortable with letting it rise at room temperature overnight. If you do that, you might need to warm up the pan before putting it in the oven to bake.

Taste, convenience, and nutrition all in one little package? Sounds like it’s time to put Morning Glory Sourdough Muffins in your breakfast rotation soon!

Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe

All the details you need to make these delicious muffins are below. Scroll all the way down for a printable recipe card with the most necessary instructions. Happy baking!

Disclosure: This contains affiliate links. If you purchase through one of these links, your cost is the same, but I can earn a commission. Thanks!

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  • 4 cups sifted whole wheat flour (I like to freshly grind mine in my WonderMill)
  • 1/4 cup ground flax seeds
  • 1 tablespoon ground cinnamon
  • 1 teaspoon ground nutmeg
  • 2 teaspoons salt (I use Real Salt)
  • 1/2 cup whole cane sugar (avoid sugar made from sugar beets as these are frequently genetically modified products)
  • 1 cup fed & active sourdough starter
  • 1 1/2 cup milk, buttermilk, or thinned yogurt (I often use sour milk)
  • 4 beaten eggs
  • 2 teaspoons vanilla extract, optional (because it’s pricey right now)
  • 1 cup finely diced apple with peel
  • 1 loose cup shredded carrot
  • 1/2 cup pumpkin seeds(sometimes called pepitas)


1. Combine flour, ground flax, cinnamon, nutmeg, salt, and sugar ingredients in a large mixing bowl. Make a well in the center. You can also mix these in a stand mixer with a dough hook or paddle attached (I often use my WonderMix). You don’t need to make a well in the center if using a stand mixer.

2. In the center well, add the sourdough starter, milk, eggs, and vanilla extract, if using.Beat them with a fork or whisk until they’re thoroughly combined, then stir in the dry ingredients until just combined. Or, if using a stand mixer, mix the wet ingredients in a smaller mixing bowl or large measuring cup, then pour over the dry ingredients and mix on the lowest speed until just combined. You will have a thick batter.

3. Stir in the apples, carrots, and pumpkin seeds, then scoop the batter into well-buttered muffin pans (I use stoneware). This makes enough for around 24 muffins, so you’ll want 2 muffin pans.

5. Let rise for 8-12 hours, or overnight. I keep them uncovered in my cold oven to avoid drafts. If you’re concerned about eggs being in the batter overnight, you can also let them rise in the refrigerator for 24 hours, covered with a damp towel. Allow the pans to come to room temperature before baking.

Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe (5)

6. When ready to bake, preheat the oven to 375, then bake the muffins for 25 minutes, or until golden brown. If you use stoneware like I do, you might need to bake an additional 5 minutes or so.

7. Cool on a wire rack for a few minutes after baking, then enjoy with some fruit, scrambled eggs, and of course, yummy butter!

If you like your muffins on the sweet side, try drizzling these with maple syrup, honey, or even an herb-infused honey when you serve them.

Additional Options

  • Replace some of the diced apple, shredded carrot, or pumpkin seeds with other add-ins like shredded coconut, sunflower seeds, or raisins (if you must, but don’t tell me).
  • Instead of baking in muffin pans, pour all the batter into a buttered 9×13 pan and bake for 40-45 minutes. We call this muffin cake.
  • Play with the spices. Reduce some of the cinnamon and nutmeg and add ginger, cardamom, cloves, allspice, or orange zest.

Printable Recipe Card: Whole Wheat Morning Glory Sourdough Muffins

Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe (6)

Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe

Yield: 24 muffins

Prep Time: 10 minutes

Cook Time: 25 minutes

Additional Time: 8 hours

Total Time: 8 hours 35 minutes

Mix up a batch of Morning Glory Sourdough Muffins at night for the perfect combination of taste, convenience, and nutrition in the morning!


  • 4 cups sifted whole wheat flour
  • 1/2 cup sugar
  • 1/4 cup ground flaxseed
  • 2 teaspoons sea salt
  • 1 Tablespoon cinnamon
  • 1 teaspoon nutmeg
  • 1 cup fed & active sourdough starter
  • 1 1/2 cups milk, buttermilk, or thinned yogurt
  • 4 eggs
  • 2 teaspoons vanilla extract (optional)
  • 1 cup finely diced apple
  • 1 cup shredded carrot
  • 1/2 cup pumpkin seeds


  1. In a large mixing bowl, combine the flour, sugar, flax, salt, cinnamon, and nutmeg. Make a well in the center and add the sourdough starter, milk, eggs, and vanilla, if using. Whisk thoroughly to blend, then stir into the dry ingredients. Fold in the apple, carrot, and pumpkin seeds.
  2. Grease two muffin pans. Fill the muffin cups around 3/4 full. Place in a cold oven to rise overnight (or allow to rise in the refrigerator for 24 hours).
  3. When ready to bake, preheat the over to 350°F/190°C. Bake the muffins for 25 minutes, or until golden brown on the sides. Enjoy warm or cooled.


You can also bake this recipe in a greased 9x13 dish for approximately 45 minutes.

Nutrition Information:

Yield: 24Serving Size: 1
Amount Per Serving:Calories: 152Total Fat: 3gSaturated Fat: 1gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 33mgSodium: 225mgCarbohydrates: 27gFiber: 4gSugar: 6gProtein: 6g

Actual nutrition data may vary.

For More Delicious Sourdough Recipes, Try These:

  • Simple Sourdough Sandwich Bread
  • Sourdough Hamburger and Hot Dog Buns
  • Easy Sourdough Drop Biscuits
  • Irresistable Whole Wheat Sourdough Cinnamon Rolls
  • The 50+ Best Sourdough Recipes That Will Have You Baking Tonight
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With all of that flavor, nutrition, and early morning ease, you can’t go wrong with these Morning Glory Sourdough Muffins.

Unless, of course, you put raisins in them.

But maybe that’s just me.

Do you have a favorite type of muffin?

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Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe (2024)


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