Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe

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.

Healthy Whole Wheat Morning Glory Sourdough Muffins Recipe

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.
Morning Glory Sourdough Muffin ingredients: apple, carrot, flax seeds, pumpkin seeds

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.

morning glory sourdough muffins with eggs and coffee for breakfast

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!

batch of Healthy Whole Wheat Morning Glory Sourdough Muffins


  • 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.

morning glory sourdough muffins before baking
Morning Glory Sourdough Muffins after rising overnight and before baking

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

Morning Glory Sourdough Muffins

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: 24 Serving 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:

Morning Glory Sourdough Muffins

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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    1. I’m allergic to ground flaxseed… Wonder if I leave it out will it alter the texture? Do I need to sub something in the place of the flaxseed?

      1. You can definitely leave it out! If the dough seems extra wet, you could add another tablespoon or two of flour to the mixture.

    2. These turned out GREAT! I baked for 20 mins (including preheating time) instead of 25 & that was perfect. Ran out of whole wheat flour, so used a 1/2 cup of all purpose to finish it off. Also used walnuts & pecans instead of pumpkin seeds. Sourdough flavor was perfect!

      I loved that I can mix these up, leave them in the oven then bake them in the morning. It was so easy!

      I expected them to be more dense but they were a great texture—much softer than I expected while still having that rustic feel and flavor.

      These are definitely going in my go-to recipes 😋

    3. What about the eggs when letting sit in oven overnight? Always told to bake something right away or refrigerate with eggs in it.

      1. Hi Lori! You can definitely refrigerate the batter if you’re uncomfortable leaving the batter out with eggs mixed in it. Step 5 shares:

        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.

        I hope that helps!

    4. I honestly make sourdough everything – these were not my favorite and I even added more sugar because the batter was so not good. They smell great- but are very dense and dry. Also do not use baking cups cuz they will not come out.

      1. I’m sorry these weren’t to your liking, Denise. I hope you can find a different kind of recipe that’s more up your alley! 🙂 Happy baking!

    5. We LOVE these. I used half a cup of allulose for sweetener. I was too tired to make muffins so I made it into a cake and cut it into smaller pieces. We’re calling it Glory Cake and it’s delicious! Thank you for the recipe!!

      1. I’m so glad you enjoy them and could make them work for your family. I love the idea of Glory Cake! 🙂 We do it that way at our house usually, too. We call it Muffin Bread, but your name is way more fun.

    6. Worst muffins I’ve ever had. And all I do is bake with sourdough and fresh milled flour. Can’t believe it, really.

      1. Hi Madelyn. I’m sorry you didn’t enjoy the muffins. We like them a lot, but they are admittedly different than the typical soft and sweet muffin. I hope you find a different recipe that you enjoy more! Happy baking to you!

    7. Loved these muffins! I used whole wheat pastry flour and they were perfect. I thought they would be plain because of the low sugar but I had one right out of the oven with butter and I loved it as is! These will be great with nut butter, apple sauce etc. I used a silicone muffin pan and no problem..

      1. I’m sorry, I don’t. As a simple home baker, I don’t weigh out my ingredients, though I realize that’s more precise.

      1. Hi Elisa. I haven’t tried the recipe with a plant-based milk, but my guess is that it would work just fine. If you try it, I’d love to hear how it works out for you!

    8. These were great! Loved the flavour, I added about 1/2 extra of sugar for a bit more sweetness and coconut flour instead of flax seeds. I also used 2 cups spelt and 2 cups white flour. As well as walnuts in place of pumpkin seeds. I also let them rise on our counter for three hours as the heat in our home is enough for a healthy sourdough to rise fully! Then popped them in the oven. Although the liners stuck to the muffins I refused to use a toxic spray oil on them. All in all, great recipe with a few tweaks of my own.

      1. So glad you enjoyed them, Emma! I think tweaking recipes is always the best way to go. I don’t think I ever leave them alone when I cook, either. 🙂

    9. Love the ease of just popping these in the oven in the morning, but the amount of sweetness was really lacking, and we don’t generally go very sweet! They tasted like plain bread muffins. The texture was nice and chewy though. I added raisins along with apples and carrots. Will try a little more sweetener next time.

      1. Sourdough breads and baked items tend to keep longer than yeasted and other quick breads, but I’d recommend storing these in the fridge if you won’t eat them all within a day or so since there’s added fruit in them.

    10. Thank you for a great recipe which doesn’t require extra leaveners/rising agents like baking soda/powder. I prefer to use just sourdough and this did not disappoint! The only modification I made was to use a about half as much nutmeg and a bit less cinnamon. I subbed cardamom for some of that too, as I love the flavor. Was wanting to use up some sauce I had made/froze from our pears, which made the dough a bit wet, so I added about a 1/2 cup more flour. Was worried they might not rise with so many wet/heavy ingredients but they had good oven spring. Next time I might also sprinkle some sugar on top prior to baking to hit the sweet note without adding much more. Thanks again!

      1. I’m so glad you liked your muffins! Your modifications sound so yummy. I love that about sourdough… it’s so flexible that it makes modifying and playing with recipes fun and easy! I think I might have to add pears and cardamom the next time I make these.

    11. not very sweet. loved the flavor the sourdough starter added to the overall effect and the texture was perfect…I just think they were a little too ‘healthy” tasting and next time I’ll use a little more brown sugar and/or orange juice to sweeten them a bit more.

      1. You can definitely do that, Teresa! We don’t like things very sweet (well… at least I don’t; a couple of my children might disagree, ha ha!), so I keep the sugar to a minimum. I hope you like the results with more sugar.

    12. Just ate one of these fresh out of the oven with plenty of butter, and can already tell I’ll make these again. These are a great breakfast: hearty, deliciously spiced, with a pronounced sourdough tang which I love. I skipped the flaxseed because I didn’t have any, added 2 tbsp olive oil to the mix, doubled the carrot to replace the apple, and added some dried cranberries. I didn’t use paper liners, just greased the muffin pan and they came out okay with some persuasion from a butter knife. I never would’ve thought of fermenting muffin mix over night, so as a low-fodmap person this recipe is a great discovery! Thank you!

      1. I’m so glad you enjoyed these, KiriAnn! And I love how you tweaked the recipe to make it work for what you had on hand. I do the same! 🙂

    13. These turned out great! I cannot have oil right now and was needing something yummy! Other recipes have a cup of oil and that is just not possible for me right now. The reduced sugar is good, too, because they get plenty of sweetness from the apples and carrots. I sprinkled a tiny bit of raw sugar on top just for the sparkle and served with fresh butter for my family. Thanks for the recipe!

    14. Thank you for the recipe. Have you made these with egg replacedr or chia – or flax -eggs? I do not eat eggs and wondered about substitutions.

      1. Hi Priscilla. Personally, I haven’t, but I don’t see any reason why you couldn’t. The dough will still rise fine thanks to the sourdough starter, but they might just be a little more bread-like when they’re finished.

    15. Adjustments a must! Definitely need some oil or applesauce. I oiled the paper liners as suggested and I had to cut the muffin away from the liners. After an 8 hour rise of of a wet batter, the liners were nicely fused to the bread – not good. Amount of nutmeg should be reduced dramatically. IMO not worth the time even with adjustments. I’ll stick to starter discard plus a bit of baking soda and get the show on the road,

      1. I’m so sorry to hear these stuck like that for you. Someone else had the same experience, so I’ll update directions to reflect that potential problem.

        We enjoy the nutmeg in this recipe as is, but taste preferences certainly vary. I hope you find a different recipe that works better for you.

    16. These were disgusting. Don’t waste your time or ingredients on this. I should know better than to try a recipe without reading reviews first. They taste like hardened oatmeal with a tang of sourdough bread. SKIP.

      1. I’m sorry to hear you didn’t like these. Our family loves them, but everyone has unique tastes. I hope you find a different recipe that suits yours soon. 🙂 Maybe you’d like one that includes more sugar and oil?

    17. These muffins were tasty but really dry. They need some form of fat in the batter other than egg in order to make them more moist and tender.

      1. Thanks for sharing your feedback. We’ve never found these to be dry, but there’s a lot of variation that can go into baking. I’m sure you could add 1/4 cup oil or melted butter and see how that works for you. 🙂

    18. I put them in papers in the muffin pan. Left them overnight and baked them in the morning. The papers stuck to the pan and then when I did get them out of the pan, the papers stuck to the muffins. Won’t be doing that again!

      1. Oh no, Deb, I’m so sorry to hear that! I do recommend spraying muffin liners with oil since the sourdough batter can stick. I hope you were able to salvage them.

    19. Can you just leave the bowl of dough overnight, and fill the muffin tins in the morning? I leave my sourdough waffle sponge overnight, stir in the eggs in the morning and then use it and it’s great.

      1. You can definitely try that, Cindy! I’ve done that before, but add 1 tablespoon of baking powder with the eggs since the batter is rather thick and will deflate when you stir the eggs in. The baking powder helps them rise when you bake them. But if you try it without adding the baking powder, I’d love to hear how it works out for you!

    20. These turned out perfectly! I’m always a bit worried when I use recipes with sourdough starter because it can be a bit unpredictable but these rose nicely with domed tops. I used a buttermilk/goat milk yogurt combo for the liquid. Delicious!

    21. These look yummy, but the prep time on your recipe is misleading as you haven’t included the hours needed to allow the dough to rise before baking.

      1. Hello Margaret. I’m sorry you found the recipe time misleading. That’s never my intent. The way my recipe card tool is set up doesn’t allow me to add in waiting time to the total, but I edited to add it to “Additional Time” so it wouldn’t lead to confusion for anyone else. Best wishes.

    22. Can these muffins be made with discard or is a bubbly starter preferred, please?
      Thank you in advance for your reply.

    23. I just did this recipe last night. Sourdough can be tricky as I’ve noticed starters differ one to another but it came together fine and wasn’t dense. The only issue I had was that I used muffin liners and there’s no oil in the recipe, and it all stuck. I had to carve them out. I think this is more a bread recipe than a muffin recipe. Also, maybe this is a late question since I already baked them but in the past when soaking or using sourdough eggs have been added the next morning before baking. Is it safe to leave eggs overnight in the dough? I know it wouldn’t be the same as you want the sourdough to rise before baking so mixing anything in the morning would deflate the dough.

      1. Hello, Katie. Regarding the eggs, you can add them in the morning if you feel more comfortable with that, and then mix in 1 tablespoon baking powder to help them rise. I personally have no problem leaving the dough to rise with eggs in it, but I know others might not.

        Thanks for letting me know they stuck to the muffin liners. I’ll add a note to grease liners with a natural oil spray if someone wants to use them.

    24. I made this recipe using mixed, dried fruits and it sadly turned out very heavy and not at all good. I used paper liners in muffin tins and the muffins were completely stuck to the paper and hard as rocks.

      1. I’m sorry to hear these didn’t turn out for you, Kathy. It sounds like your sourdough starter didn’t raise the batter very well, or perhaps the batter was too dry?

    25. Hi there! Is there any way to sub out the sugar and replace with maple syrup or honey? These look great, thank you!

      1. Hi there, Madileine. You could certainly toy with the recipe to use liquid sweetener instead of sugar. Honey burns easier, so generally it’s suggested to reduce the oven temp by 25 degrees if baking with honey. You might have to reduce the other liquids in the recipe a bit, too. Perhaps try 1 cup buttermilk instead of 1 1/2? I haven’t done this, but this is where I’d start if I were to tinker with the recipe and try. I’d love to hear how it works for you if you switch the sweeteners!

    26. Hi there! I am new to the sourdough world and so exited to try this recipe! I was wondering if I could substitute whole wheat flour instead of whole grain flour (all I have in my kitchen at the moment)? Do you think that would make a big difference? And my starter is a bit thick, so should I add some extra milk to thin it out? Thanks!

      1. Hi there, JoAnna, and welcome to the wonderful world of sourdough! Yes, you can certainly use whole wheat flour. Any whole grain will do. I like to use a mix of whole wheat and whole oat flour, but whole wheat is just fine. If your starter is thick, you might need a little extra milk. Maybe an extra 1/4 cup, depending on how thick it is. Have fun and enjoy!

        1. Thanks for sharing these recipes. I’ve tried making the morning glory muffins twice now with no success.. They turn out as hockey pucks each time. I really like the long fermentation style muffins for the gut health of our son. Any suggestions would be greatly appreciated.
          My other types of muffins turn out great

          1. Hi Bergman. That’s a bummer! I’ve made some hockey pucks before, too and it’s always a bummer. It’s so hard to say exactly what might be going on without seeing the whole process, but a few things come to mind. It could be your starter isn’t active enough when you add it to the recipe (but it sounds like you do other sourdough baking, so I’m guessing this isn’t it). Usually, if my sourdough items turn out too dense it’s because my dough had too much flour in it. So that’s an idea. The last I can think of is perhaps you can try using fewer add-ins? I hope one of these ideas helps!

    27. These look AMAZING! 🙂 I love that you mix everything in, put it in the muffin tin, and then let it rise overnight. So easy!

    28. I love your series about sourdough and have been inspired to try. Have you ever made these muffins with blueberries?

      1. Hi Dawn! Yes, I’ve made all sorts of muffins, including blueberry. I use the same basic dough, then leave out the cinnamon and sometimes nutmeg, maybe add in some orange or lemon zest, etc, and of course add the blueberries! Depending on the type of muffin, sometimes I’ll add more sugar since these are just slightly sweet. Hope that helps!