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These wholesome morning glory muffins are my very favorite muffin variety. Filled with healthy ingredients like whole wheat flour, flax, apples, carrots, raisins, applesauce, and honey, these cinnamon-spiced muffins taste like apple cake, spice cake, and moist carrot cake combined. (And for breakfast!) There’s plenty of substitution suggestions available so you can truly make them your own.

morning glory muffins

Do you remember when I first shared this recipe? It was back in 2015 and we’re revisiting it now because it continues to be a healthful breakfast favorite. I simplified the instructions and added plenty of substitutions so you can play around with the recipe. They’re my best morning glory muffins and here’s why you’ll love them!

These Morning Glory Muffins Are:

  • Deliciously moist and spiced, just like pumpkin muffins
  • Mega flavorful with hints of orange
  • 100% whole wheat
  • Healthier and wholesome
  • Satisfying and hearty
  • The perfect on-the-go snack
  • Toddler-approved (victory dance!)

Plus, there’s no mixer required—just use a whisk and they freeze beautifully!

morning glory muffins
morning glory muffins

Are These Muffins Healthy?

The term healthy is, of course, all relative. But I would consider them on the healthier side, yes. They do contain wheat, some oil, and some refined sugar, but also healthful ingredients like fresh fruit and vegetables, applesauce, flax, honey, and whole wheat flour. Balance! I like to use some applesauce in place of some oil, just like how I replace some butter with unsweetened applesauce in my baked oatmeal. They are similar to my applesauce muffins where the lighter ingredient replaces some fat while still keeping them extra moist and flavorful. (I don’t recommend replacing ALL the oil here—the morning glory muffins will taste rubbery.)

Think of these as my reader-loved Harvest Spice Bread, but in muffin form. 🙂

morning glory muffins ingredients and batter
morning glory muffin batter in muffin pan

How to Make Morning Glory Muffins

If you felt confident enough, you could probably make these with your eyes closed. I have the recipe memorized by now!

Making these morning glory muffins is as simple as combining all the dry ingredients in 1 bowl, combining all the wet ingredients in another bowl, then mixing everything together by hand. The batter is relatively thick and chunky because of all the flavorful add-ins, but this makes spooning into muffin liners pretty easy.

You need a shredder/grater for the carrots and apple. I always use my box grater, which doubles as a cheese grater. This tool is handy for zucchini bread, healthy apple muffins, zucchini muffins, carrot cake, and grating frozen butter for my scones.

18 Ingredients, but Don’t Worry!

I know the list of ingredients in the recipe below looks overwhelming, but most of them are regular kitchen staples like flour, salt, baking soda, cinnamon, eggs, brown sugar, and vanilla extract. For all of the extras, there are plenty of substitutions you can make.

The orange zest and ground flax are totally optional, but I usually add both for extra flavor.

healthy morning glory muffins
morning glory muffins

Ingredient Variations/Substitutions

Here’s a list of ways you can change the recipe based on your tastebuds. If using any of these substitutions, use the same exact amount of the ingredient you are replacing unless otherwise noted. For example, if you use coconut sugar instead of brown sugar, use 1/2 cup.

  • Whole Wheat Flour: Use all-purpose flour if desired instead. I haven’t tested this muffin with gluten free flour alternatives, but I would steer clear of almond, coconut, and oat flours. They won’t hold up to the moisture in the batter. (Try my blueberry almond power muffins instead!)
  • Pecans: Leave them out or replace with dried cranberries, chopped walnuts or pistachios, sweetened or unsweetened shredded coconut, sunflower seeds, or more raisins.
  • Brown Sugar: Coconut sugar is a dry unrefined sugar you can use in its place.
  • Honey: Brown sugar, coconut sugar, or pure maple syrup.
  • Oil: Melted butter. I don’t recommend leaving the fat out completely.
  • Applesauce: If needed, replace with melted butter or more oil, apple butter, mashed banana, canned crushed pineapple, or pumpkin puree.
  • Orange Zest: You can leave it out.
  • Orange Juice: Delicious flavor! You can use pineapple juice or milk instead.
  • Raisins: Leave them out or replace with dried cranberries, other chopped dried fruits, sweetened or unsweetened shredded coconut, chopped walnuts or pistachios, sunflower seeds, or more chopped pecans.
  • Carrots: Feel free to replace with more shredded apple or even shredded zucchini.
  • Apples: You can replace with shredded zucchini or more shredded carrot. I also love replacing the 1 cup of shredded apple with 2/3 cup canned crushed pineapple.

I have tested all of these options. Anything not listed, I haven’t tested myself so use caution! I will say that this is a very forgiving muffin recipe. Have fun with it!

healthy morning glory muffins

More Healthful Baked Goods

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Morning Glory Muffins

Morning Glory Muffins

  • Author: Sally
  • Prep Time: 30 minutes
  • Cook Time: 24 minutes
  • Total Time: 1 hour
  • Yield: 1416 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


Filled with healthy ingredients like whole wheat flour, flax, apples, carrots, raisins, applesauce, and honey, these cinnamon-spiced morning glory muffins taste like apple cake, spice cake, and moist carrot cake combined. (And for breakfast!) There’s plenty of substitution suggestions available above so you can truly make them your own.


  • 2 cups (260g) whole wheat flour (spoon & leveled)
  • 2 teaspoons baking soda
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon ground ginger
  • 1/2 teaspoon salt
  • 1/3 cup (35g) ground flax (optional)
  • 3 large eggs
  • 1/2 cup (100g) packed light or dark brown sugar
  • 1/4 cup (85g) honey
  • 1/3 cup (80ml) vegetable, canola oil, or melted coconut oil
  • 1/3 cup (60g) unsweetened smooth applesauce
  • 1 teaspoon orange zest (optional)
  • 1/3 cup (80ml) orange juice or pineapple juice
  • 1 teaspoon pure vanilla extract
  • 2 cups (260g) shredded carrots (about 4 large)
  • 1 cup (140g) shredded/grated apple (about 1 large)
  • 1/2 cup (75g) raisins
  • 1/2 cup (64g) unsalted chopped pecans


  1. Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or use greased/sprayed cupcake liners. This recipe yields 14-16 muffins, so prepare a second muffin pan in the same manner or bake in batches and reserve leftover batter at room temperature for when the first batch is done.
  2. Whisk the flour, baking soda, cinnamon, ginger, salt, and flax together in a large bowl. In a medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce, orange zest, orange juice, and vanilla together until combined. Whisk in the carrots and apples. Pour these wet ingredients into the dry ingredients, stir a few times with a wooden spoon or rubber spatula, then add the raisins and pecans. Fold everything together just until combined and no pockets of flour remain.
  3. Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425 then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 23-24 minutes, give or take. (For mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.) Allow the muffins to cool for 10 minutes in the pan, then transfer to a wire rack to cool until ready to eat.
  4. Cover leftover muffins and store at room temperature for 2 days or in the refrigerator for 1 week.


  1. Make Ahead & Freezing Instructions: Muffins freeze well for up to 3 months. Thaw overnight in the refrigerator and warm in the microwave (if desired) before enjoying.
  2. Substitutions: See blog post above for all substitutions I’ve tested.
  3. Initial High Temperature: The burst of very hot air will spring the top of the muffin up quickly, then lower the temperature as instructed so the inside of the muffin can bake through. This helps the muffins rise nice and tall. I do this for all of my muffin recipes.
  4. Nutritional Information: I haven’t calculated it, but feel free to use a free online recipe calculator with the exact ingredients you use.

Keywords: morning glory muffins

Reader Questions and Reviews

  1. Made these amazing muffins today for the first time. I was able to eat one….there are only six out of fourteen left. Three of us in my family. LOL thank goodness there is enough for tomorrow morning. They are by far the best morning muffins ever!!!♥️♥️♥️

  2. These look delicious! My kids are incredibly picky (Sigh) Do you think I could use carrot purée (baby food) in place of the carrots?

    1. Hi Jennifer! We haven’t tested carrot puree, but see the blog post above for all our recommended substitutions.

    2. U can delete and substitute easily in this recipe. I add chopped figs to mine. Just be aware of the moisture content when u substitute.
      This truly is the best morning glory muffin recipe I’ve found!

  3. this recipe is really really good!! I like to pplay around and substitute things in recipes so this one is right up my alley. The next batch i intend to add a bit of lemon zest which i think will give them an interesting taste.

  4. So, I admit that I completely left out the oil in these by mistake, and two different reviews from recipients came in that they were still moist and delicious! Now I am curious what the purpose of the oil is in this recipe and how would it have made them come out differently?

    1. Hi Alison! The oil will add more moisture to these muffins, but we’re happy to hear that they turned out even if left out 🙂

  5. Yummy! And can confirm toddler approved. He ate 2 straight from the oven. Thanks again for an amazing recipe.

  6. I’ve made the recipe a couple of times turning them into gluten free, nut-free, vegan morning glory muffins. They have been absolutely delicious. Craved by all I’ve shared them with including those who aren’t vegan, aren’t allergic to nuts and don’t need to eliminate gluten from their diet.

    My substitutions include using a 1:1 gluten flour (multiple brands have worked well), 1/2 cup pumpkin (125g) in place of 2 of the eggs, 1/4 c unsweetened applesauce (55g) for one of the eggs and unsalted sunflower seeds instead of pecans. The muffins are EXTREMELY moist without the eggs so I’m experimenting with how much LESS juice to put in. When I used the full 1/3 cup of juice I ended up cooking the muffins at 350 for almost another 20 minutes until the insides weren’t kind of gooey. If someone else has figured this part out I’d love your recommendation on how much juice to use.

    1. I traditionally don’t make morning glory muffins with juice, so I bet you could leave it out entirely and it would still be great! Good luck!

  7. My husband and I travel in our fifth wheel. These sound delicious and I want to make them but I have a convection oven that can also be a microwave. I have no regular oven. Does anyone have any ideas how long I should cook these with the convection oven?

    1. Hi Deborah, if you do use convection/fan settings for baking, we recommend lowering your temperature by 25 degrees F and keep in mind that things may still take less time to bake.

  8. Sally

    Awesome recipe

    Used chopped walnuts and pecans. Dried cranberries instead of raisins. Topped with crushed roasted unsalted almonds and a sprinkle of “sugar in the raw” on top before baking.

    Had great reviews!

    I’ve also made your blueberry muffins (also great!)

    My wife tells me I should start a muffin shop (hopefully kidding – I’m recently retired)


  9. Recipe was a WINNER! Substitutions: aquafaba for eggs, pumpkin for applesauce and coconut sugar for brown sugar. Followed instructions and it was delicious. I even added coconut to the many other ingredients. I will make this again!

  10. Thank you! These muffins turned out so well! So good for specific instructions on how full to fill the tins and the initial high heat to get spring. Appreciate the relatable amount instructions (about 4 carrots). Also the suggestions for substitutions were helpful. I think I love most the fresh orange juice plus zest. My substitutions for today were 1/4 C almond flour in place of 1/4 C ww flour and slightly ground oatmeal in place of flax seed. Very delicious!

  11. These muffins are delicious! I was missing a couple of ingredients, so I made some substitutions that were suggested in the recipe. I used all Apple, because I have no carrots, and I used pineapple juice instead of orange juice. These were super delicious! I love the trick of the blast of heat right at the beginning. Your recipes always so good! Thank you for testing them well and not making them overly sweet!

  12. I love the recipe. thank you.
    I made it twice, 1st time with a half recipe with AP Flour baked in a Madeleine pan, Taste was really good but they were very soft and very moist not like muffins
    2nd time, half recipes with WW Flour, Test, and structure were much better but still very very moist.
    Everyone who’s tried both like the taste but they said they were not muffins.
    I am wondering, is it because I baked them in the Madeleine pan that why they were so moist?
    what can I do to make it less moist? Thanks.

    1. I recommend using a muffin pan– after greasing a madeleine pan, it can hold a lot of butter/grease and I imagine the batter wouldn’t have enough room to properly cook.

    1. Hi Jill, For jumbo muffins, bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-30 minutes or until the centers are set. Stick a toothpick in the center of a muffin to test for doneness.

  13. I am eating one now and they were perfect. Time and effort to make these are worth it. Better then any baker around here. The fact that they are not being made by any baker within a 30 mile range prompted me to make it myself. Came upon this recipe and it looked like a lot of hard work. Got a helper and never looked back. Thank you for this awesome muffin. I am keeping this in my safe spot.

  14. These look delish! Wondering if you’ve ever baked this batter as a loaf and how I might adjust temp/time for that? Fam isn’t a big fan of muffins, but think they would love this as a morning bread!

    1. Hi Veronica, you can bake this in a 9×5 loaf pan without making any changes to the recipe. We’re unsure of the best bake time, but use a toothpick to check for doneness.

  15. Love these! I used 3/4 cup Truvia brown sugar and they were great!!

  16. Thank you for your recipe! What do you think about using 1/2 unbleached flour and 1/2 whole wheat?

    1. Hi Molly, you sure can! Hope you enjoy the muffins.

  17. I’ve loved Morning Glory Muffins for years, but never found a recipe until now. I’m so happy to have seen it here. Scrumptious! And versatile with all the substitutions that can be made. Thanks!

  18. Sally if I freeze the raw batter do I use the same baking instructions, starting out with the high heat then lowering the temperature? Thank you.

    1. Hi Mary, we don’t recommend freezing the raw batter. But the bakes muffins freeze beautifully! See recipe notes for details.

  19. Would like to add unsweetened, unsulphured shredded coconut and sunflower seeds. What should cut back on?

    1. Hi Barb, you can replace the 1/2 cup pecans and/or the 1/2 cup raisins with the same amount of coconut and sunflower seeds.

  20. i made these today and my 6 year old loves them. As I type he’s already on his second one.
    I use spelt flour instead of whole wheat. I ended up using the pineapple juice option because I had canned pineapple and I also chopped up about half the can and threw it in there. I did not add any nuts. I also don’t keep brown sugar in the house, so i did a combination of sugar and molasses. The result are very good; a not overly sweet muffin that I can happily give to the family for breakfast.

    Thanks again for another great recipe!

  21. These turned out great, I followed the recipe almost exactly, but left out the nuts. My toddler goes, mmm when he eats each bite. My only question is why are there little green flecks in the muffin, when I did not use any green ingredients? Could the pineapple juice have reacted with the carrot or apple?

    1. Hi Lynn! This is usually a reaction from the baking soda and shredded carrots– give it a quick internet search. It’s normal!

  22. The versatility of this recipe is fantastic! I substituted a few items and added a few extras of my own. They still rose beautifully and were super moist. So nutritious and delicious! Thanks

  23. These are the best muffins I have eaten. I will make them often. Thank you!
    During Covid I have been baking a lot of different muffins. By far this is the very best recipe. Thanks for sharing it

  24. I haven’t tried them yet, I’m sure they’ll be great. Everything I make from this page is. Just did the calculations for calories. Unless I forgot or miscalculated, It’s about 3,620 for the whole batter and about 226 per muffin which is really good considering most muffins you get are closer to 400. Really excited for these.

  25. These are delicious! I made them to give my toddler and she devoured them! Next time, can I skip the brown sugar or would that mess with the texture? Also, they came out pretty soft, how can I make them firmer? Only change I did was use zucchini instead of carrots.

    1. Hi Ann! Sugar is used for moisture and texture in baked goods as well as taste. You can certainly try reducing the sugar, but the resulting texture will be different than intended. Is it possible the muffins were under-baked? They shouldn’t be overly-soft. Thank you for giving this recipe a try!

  26. These muffins are soooo delicious and so versatile! I only had plain flour on hand, also had to use milk instead of OJ and walnuts instead of pecans….results were perfect. I also accidentally added the apple, raisins, nuts and carrots to the wet ingredients, before adding to the dry, but it didn’t hurt anything! Will make these many times I am sure!

  27. Great recipe, I added carrots, zucchini and apples to total to 3 cups. Should I have squeezed some of the liquid out of the zucchini they seem a bit too moist. Added some chopped dried apricots too. Delish!

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