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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. Hi Mandy, 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.

    1. Hi Katie, Yes you can peel and then shred your apple. We hope you enjoy these muffins!

  1. Excellent. Used mashed banana instead of applesauce (thank-you for that option), added half a cup of chopped fresh cranberries, omitted the pecans and sprinkled a few salted pumpkin seeds on top instead.

  2. Absolutely delicious! Wouldn’t change a thing . I’m not a fan of whole wheat as the things I make with whole wheat tend to come out dryer and dense — but not so with this recipe. I have made these as mini- muffins several times and it has never failed me – super moist, fluffy and super delicious. I have been meaning to try freezing a batch for later, but they’re gobbled up by the kids (with a little help from me) each time. Thanks for a great healthy little snack/treat! – Wonderful recipe — it’s a keeper !

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

  3. Thank you so much for this wonderful recipe. Morning glory are my favorite muffins and I have been looking for a “healthier” version for a while. I made some substitutions based on preference and what I had on hand. Wheat germ for flax, 1 cup zucchini for 1 cup of the carrots, and 1/2 cup yogurt for the applesauce and honey, as I suspected the recipe was a little sweet for my taste. I also added shredded coconut. I especially like the fluffy texture and the domed top. This is my first recipe from this site but I will be back.

  4. Thanks for this amazing recipe! I didnt have enough carrots for the double recipe so I did 3 cups carrots and 3 cups apple. Didn’t have applesauce so I substituted Pumpkin purée and added 2 tsp pumpkin spice instead of the extra cinnamon. I didnt have flax seed so I substituted large rolled oats. The batter seemed a bit too wet so I added in 1 cup of large rolled oats in hopes that it will soak up some of the moisture. These are so tasty! So much flavour and texture. I will definitely be making these again!

  5. I substituted the flour for buckwheat flour. This recipe turned out beautifully!! <3 <3 <3. Thank you sooo much for the recipe. You are definitely a gifted baker!

  6. Just made these muffins and they are delicious. I cut the brown sugar only by a couple tbsp or so and they were plenty sweet for us! Next time I’ll add unsweetened shredded coconut for that extra chewy factor. 😉 I will also shred the apple instead of chopping it. Recommended cooking time was spot on.

  7. Followed recipe exactly, I’m an experienced baker, but at 19 minutes for the second step these were over-done. Too dark, dry. Disappointed. I have a convection oven but maybe I needed to shorten the first step at the hotter temp in addition to the second step.

  8. Sometimes I wonder why I even have a Pinterest account. I always end up choosing the Sally’s Baking Addiction recipe! I should just start here! Can’t wait to make these!

  9. Delicious! Tender and moist, and just the right sweetness level for breakfast. I made these to bring to a friend who just had a baby, with a few substitutions:
    – Reduced flax to 1/4c
    – Added 1c rolled oats
    – 1/3c apple sauce is only slightly less than a single-serve to-go apple sauce, so I just added the full container
    – Added pepitas to the top before baking
    – I forgot to turn down the oven after 5 min, but turned it down after about 15 and they still came out fine
    – Baked in a jumbo muffin tin (was enough for 11 muffins, roughly 6 tbsp in each)

    1. I always add grated zucchini and tonight I substituted coconut milk for the applesauce, walnuts and dried cranberries. They are super yummy! Breakfast for the week makes me so happy!

  10. These came out perfect. I left out the brown sugar. For a breakfast muffin they were sweet enough with just the honey. And I only had flax+chia mix, which worked fine.

  11. Love this recipe! Made them with regular flour and milk, no flax or raisins and came out delish! Thanks!!

  12. Love this recipe! I did 1 1/2 c flour and 1/2 c oats versus the 2 c flour, added chia seeds, used the substitutes of apple cider, pureed pumpkin and golden beets! Also used about 1/3 less of the sugar and didn’t use honey, which worked fine for my taste! Used two Tsps of pumpkin pie spice and added some turmeric for an extra golden hue 🙂 Opted for add ins like dried cranberries and pumpkin seeds. . . loved the room for creativity in this recipe! Thank you, Sally!

  13. This recipe yielded 14 muffins for us, and they were tall and bulbous on the top! So wonderfully adorable! Just ate one right out of the oven, about to eat a second.
    These are delicious! I didn’t have any ground flax so I threw in 2 tablespoons of chia seeds.
    Didn’t have apple sauce so I just added a bit more extra grated apple and a bit more oil.
    I cut down the brown sugar slightly, and I think I can cut it down some more. I used the full amount of orange juice but these came out so moist (almost TOO moist) so I may cut down on that next time too. I love how adaptable this recipe is! Will throw a few into the freezer to test how these will reheat straight out of the freezer (wanted this to be a freezer batch breakfast item that can just be microwaved).

  14. Whenever I’m looking for a recipe on google and this website comes up in the results, I know it’s going to be a good one. This recipe is no exception! I love how bright and orange-y these are!

  15. These are my favorite muffins as I’ve stated before. I just made them using puréed fresh pineapple and mango in place of applesauce and I threw dried apricots in chopper until raisin size and also subbed lemon extract for vanilla. They are DELISH! No matter what combination of ingredients I use they are always moist and flavorful.

  16. I first tasted these Morning Glory muffins at my friend’s house, and then hounded him for the recipe… and I tried making these muffins tonight. The only modifications I made were to use organic whole wheat spelt flour and I also soaked the raisins in a dark rum while I prepared the dry and wet ingredients. Knee-buckling good, and I am already planning the next batch – I might add some cacao nibs next time. Thank you, Sally.

    1. Baking can lead to some flops & I had one of those moments. I found the the melted coconut oil/butter on the counter, after the muffins had made their way to the oven. It’s true, they would have better texture and taste with this added, but all was not lost. I think the applesauce and moisture from the carrots helped! The taste was still good. I can only imagine how much better they will be with oil added!

  17. Thank you! Fantastic new recipe for our house! I have a keeper bran muffin recipe I always use, but my store was out of bran flakes for quite a few grocery trips. I found this healthy whole wheat muffin recipe as an alternative. I made them exactly as directed, except I added two teaspoons molasses, just cause I like it. Wow, wow, wow! Perfect texture, mounded, moist, and oh so tasty. Can’t wait to try the crushed pineapple substitute too.

  18. Thanks for this Recipe!! Can this recipe be replaced with apple juice instead of orange/pineapple juice?

  19. Absolutely delicious!!!! I am not clear about flax seed vs ground flax tho.

  20. This recipe was fantastic! I will definitely be using it again. I added chopped walnuts to the mix and got a wonderful crunch on the inside as well, and finished off the top of each muffin with more pecans before putting into the oven. Delicious!

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

  21. Hi Sally — I just found your Morning Glory Muffin recipe on line. I am gathering my ingredients and was very happy with your wide choice of substitutions. Can you please tell me the oven temperature(s) and baking time for Jumbo-size muffins? I will make standard size for my first try, but have an occasion where I need Jumbo muffins, and I think your Morning Glory Muffins will be perfect. Also, do you have any suggestions on how to package two muffins in a pretty way, also keeping them fresh, for gift giving. I’d like to share some with my neighbors who have been stuck inside due to Covid. Thank you for this wonderful recipe.

  22. Really enjoyed these muffins very moist added dried cranberries and blueberries

  23. I love this recipe for a hearty muffin. I like adding shredded coconut or Chia seeds as well. I also add homemade applesauce sometimes instead of the apple.

  24. Hi Sally, I love everything you do… I have never had a miss with any of your recipes.
    That is why I’m putting in a request for a Sally’s baking addiction “Maple Pecan muffin”. I have tried from other online recipes but nothing comes close to a Sally quality recipe.

    1. Hi Jennifer! A maple pecan muffin sounds delicious and certainly something I’d love to try sometime. Thank you for the suggestion and very kind comment!

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