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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
  • 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, 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. Great recipe. I used 2 eggs and 1/3 cup mashed banana for the third egg. Didn’t have any carrots or chopped apple still a great muffin . will make again. I used 170 grams regular flour with 20 grams crushed graham crackers crumbs and 20 grams dryed mashed potato flakes and 30 grams crushed cheerio cereal. Im glad you list weights also.

  2. I made these GF with a couple modifications and they were tasty. I used King Arthur Measure for Measure gluten free flour and no flax seed and these came out delicious. I also added a teaspoon of King Arthur chai spice mix to increase the spice flavor and used dried orange peel instead of zest. Used chunky applesauce because I used zucchini instead of apples. Definitely a keeper

  3. Wow. These are the best morning glory muffins I have ever tasted. They’re now my new favorite muffin recipe of all time! I wanted you to know that I’ve featured this recipe on my blog in one of my Recipe Reviews. Here’s the link if you would like to check it out. 🙂 Thank you Sally for making so many awesome recipes!

    1. Hi Sarah, We’ve never tested this recipe as a Bundt cake. It may be a bit short but it should work. You can try adding two batches, but that’s likely a bit too much batter so you could make some muffins with the excess batter. You can also 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. Let us know what you try!

      1. I made it as a loaf in an 8×4 ish pan, and it took 55 min to bake. Delicious!

  4. I love these muffins!! Every single substitution I’ve ever made in this recipe tastes good and works out. I love to make them with double raisins instead of nuts for my toddlers and with a mixture of shredded zucchini and carrots. Most recently I did 2 cups of zucchini and 1 cup of carrots and they are wonderful. Perfect amount of spice and perfect amount of sweetness. Thanks for this recipe!

  5. So fun mixing it up! I added sunflower seeds and a banana and it turned out great! Keeper!

    1. Hi Brittany, absolutely! For mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.

  6. I just made these exactly as the recipe states (minus the optional flax) and I baked them for double the time and they still seem very uncooked. I understand these must be moist due to the water in apples and carrots but they seem raw still. What did I do wrong??

    1. Hi Sarah, have you used a toothpick to test for doneness? If the center comes out clean, the muffins are done. You’re right, they are very moist muffins but shouldn’t take double the time to bake through. Thank you for giving this recipe a try!

    1. Hi Melissa, We haven’t tested this recipe with any egg substitutes, but some readers have reported success using flax egg replacement in some of our muffin recipes. If you give anything a try, we’d love to know how it goes!

      1. I’ve used these with 1/4c plain carbonated water (from my soda stream) to replace each egg. Worked great! Saw this tip online somewhere. Absolutely love this recipe!

  7. Hi i just want to ask whole wheat flour can i use bread flour or just normal one is ok

    1. Hi there, instead of whole wheat flour, you can use the same amount of regular all-purpose flour. We don’t recommend bread flour.

  8. These were delicious and I will make them again. I only had to bake for 13 minutes once I lowered the temperature to 350 degrees. They were a little dry so what can I do to increase moisture next time?

    1. Hi Louise! Be careful not to over-bake (the most common culprit for dry muffins) and be careful to spoon and level instead of scooping your flour when measuring. These tips should help for next time!

  9. Recipe sounds delicious. I’d like to try adding crushed pineapple. Would I reduce the amount of carrots?

    1. Hi Christine, you can simply replace the applesauce with the same amount of crushed pineapple. No need to reduce the amount of carrots.

  10. On the fence btw 3 and 4 stars as these were just ok. With all these ingredients, I expected these to be ‘knockout muffins’ but sadly not. Next time I will increase the sweetness and they also seemed to be missing something else ….not sure what but will research. They baked up well and looked delicious but the taste just wasn’t anything special.

    1. I felt the same as Ginny, expecting that with all these fantastic ingredients, the muffins would be fantastic. I think they could just use a bit more sugar/sweetness. I will try them again with an additional 1/4 cup sugar next time. Thanks

    2. I made these and I felt similarly because I forgot the orange zest in the first batch of muffins, and for the last 5 muffins I remembered the orange zest. Wow, what a difference with the orange zest! It really elevates the whole muffin. Don’t skip the orange zest!

    3. A bakery that I used to frequent made these with an orange glaze and it was delicious. Simply mix a bit of orange juice with powdered sugar to a thin consistency and spoon over top while slightly warm. The thin glaze will set as they cool and add a yummy sweet citrus flavor.

  11. These are the embodiment of fall! And it actually feels GOOD to eat these vs coffee shop junk.

    I love the forgiving substitutions most of all! I tried one more because I wanted to up the fiber a bit.. i subbed 1/2cup wheat bran for 1/2cup flour and I could not detect a difference!

    Another winner, Sally! Thank you!

    1. Thank you! I recently bought a bag of oat bran but didn’t know how much bran I could add to a recipe without turning it into a “breakfast muffin”. Small steps 🙂

  12. Oh my goodness! These are so amazing Sally, what a great recipe. Myself and my family enjoyed this as a nice treat. These were easy to make with minimal steps and preparation which is always great. These were delicious and will definitely make them again! 10/10. My only tip is that watch the time because I found that 20 minutes was too long after turning down the temperature, I ended up doing 15 minutes to make sure they didn’t burn. Overall, a lovely bake and reward.

    1. Hi Kirsten, we haven’t tried it ourselves, but many readers have reported success with that swap. Let us know how it goes!

  13. Recipe as written is 201 calories each for 16 muffins. Agree with the sweetness factor but a little bit of honey on top takes care of it.

  14. these muffins are divine! a great way to use up CSA produce (zucchini and carrots, this time). i doubled the recipe and ended up with abt 500g of zucchini and 300g of carrots, and i used grated apple instead of applesauce. i’m almost out of ww flour so i went 75-25 all-purpose with no ill effects. i used apple cider instead of orange juice, a mix of neutral oils (olive + avocado), and pumpkin pie spice. added some leftover sliced almonds, sunflower seeds, and dark chocolate chips. stoked to have these in the freezer!

    1. oh, and i cut the sugar quite a bit–used about 3/4c brown sugar for a double batch and omitted the honey. i think i used too much cloves, but the chocolate chips are plenty sweet enough!

  15. These are delicious, perfect moisture, and not too sweet. For those saying they aren’t sweet enough think of these as leaning more towards a savory muffin than a sweet one. I loved all of the substitution options as I added some chopped pineapple from the freezer and did 1 cup carrot with 2 cup shredded apple. I made muffins, which were good but the best were the mini loaves – so adorable and great as a gift!

    1. Hi Lois, you can omit the cinnamon or replace with cardamom, nutmeg, or ginger for a similar warm spice flavor.

  16. Fabulous recipe! Love the options. Made tonight for several friends and felt good to take a healthy option treat! Thank you for all your tips. Made a loaf of your apple cinnamon bread for another friend. It’s also one of my favorites.

  17. Hi Sally,
    I love these muffins, have made them a few times. I was wondering if I could just make it as a bread? And if so, would cooking time be a lot different than when making muffins?

    Thank you,


    1. Hi Maria, Yes, 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.

  18. Hi Sally, could you substitute oatmeal for whole wheat flour? Making these for a nursing mother.

    1. Hi Linda, it would take a bit of recipe testing to ensure results, as oatmeal absorbs wet ingredients differently than whole wheat flour. You may like these blueberry oatmeal muffins instead or you can leave out the berries in the baked oatmeal and add shredded carrots and apples, along with some ground ginger (there’s cinnamon already there!) and raisins (and/or pecans), too. Enjoy!

  19. These muffins turned out perfectly with only one substitution! I used 2 cups of Better-Than-Cup4Cup-Gluten-Free-Flour-Blend instead of the 2 cups of whole wheat flour. We love the taste! Definitely a favorite and often given as gifts to my friends who are on a GF diet.

  20. Fabulous muffins, I added 1 cup of mixed nuts on top, no change in baking time.

  21. I wanted to love these as I am looking for a healthy version of Morning Glory muffins. I followed the recipe and they looked lovely but were dry. My husband immediately said “they need more oil.” I always replace all the oil or butter with applesauce in loaf breads (ex., banana) without sacrificing moistness. Not sure what to do with these because I think the recipe has potential. I’ll try again, maybe add a banana or more applesauce

  22. Absolutely wonderful recipe. I will be making these from now on. They are very tasty and moist and healthy. I love the combination of the cinnamon and orange zest. I substituted oat bran for the flax and raspberries for the raisins. So good!

  23. Just mixing these up. The addition of the ground flax would add a big difference in the moisture of the muffin. You list it as optional. I’m wondering if they would be gooey without the flax. Anyone make them without flax?

    1. Hi Heidi, We’ve made them both ways many times and never had them be overly gooey. When you bake them just test them by inserting a toothpick in the center and bake until it comes out clean.

  24. I love these muffins. I used Amber Maple Syrup instead of honey and cut Medjool dates instead of raisins.
    They were moist and wonderful. I brought them to work and everyone loved them.

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