Morning Glory Muffins

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. My husband and I had just celebrated our 6 month anniversary at a beautiful bed and breakfast in northern Virginia. One morning we were served the absolute BEST muffins. Now, I know the trip was filled with champagne and dessert and all things celebratory, but the muffins truly stuck out to me. They were packed with apples, carrots, brown sugar, pecans, spice, raisins, and more. Basically everything I love in one.

I bake this copycat version all the time and I just updated some of the photos. I also simplified the instructions and added plenty of substitutions so you can play around with the recipe too. 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. 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 mintues
  • Cook Time: 24 minutes
  • Total Time: 1 hour
  • Yield: 14-16 muffins
  • 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 muffin sheet, 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


  1. Thank you for the recipe, these muffins were soo good! I was inspired by all your variations, and I’ve hit upon something the fam really likes. I use the pulp from our juicer after I make carrot apple juice ( After peeling and removing seeds) instead of the grated carrot and apple called for in the recipe. to make up for the lack of moisture, I just add crushed pineapple in 100% juice instead of the applesauce, and don’t drain the fruit. I also used hemp protien powder instead of some of the flour, to up the satisfying density of these treats. This is a great recipe to use the leftovers from our juicer to make something else that is really tasty.

    1. Sounds delicious, Miranda! Thanks for sharing your version.

  2. Marina Caraway says:

    Made these with our garden zucchini in place of carrots and maple syrup instead of honey and they were perfect!  I love having my recipes from your site always turn out just like they should!  This recipe is a keeper.

  3. i made these today and they are AMAZING!! I made 46 mini muffins. My son just started kindergarten and they are the perfect little snack…thanks for the recipe

  4. These are delicious, and this recipe will replace my current one. They came out very moist and cake-like. I used all whole wheat flower and pumpkin seeds instead of the pecans. Next time, I will leave out the honey and replace it with a ripe, mashed banana. They were not overly sweet, but reducing sugar more will not hurt these. Thanks for the recipe!

  5. Judith Barbiaux says:

    I just made these, used whole wheat flour, agave nectar, 2/3 cup coconut oil, 1/2 cup dried cranberries, 1 cup shredded carrots, 1 cup shredded zucchini, applesauce, half an apple grated, 1/2 cup dried sunflower seeds (goodies), just sensational.  Otherwise followed the recipe exactly.  Many different flavors blending together.  Highly recommend this recipe!  Very versatile.  

  6. Can I just say thank you SOO much for noting so many different variations and options. At first i was deterred because I didn’t have some of the ingredients on hand. You made it so easy for me to make these no matter what I have in the pantry!  

    1. Glad you find it helpful!

  7. Wow! These are delicious! My step-son loves these for breakfast. I will make them over and over again, I’m sure. Thanks for the recipe

  8. Hi Sally. 

    Can this batter be put into a loaf pan? Thanks!

    1. I can’t see why not! Unsure of the bake time though.

  9. The best muffins I’ve ever made! I’m going on a one day trip to capital tomorrow with my classmates, and since we all agreed on bringing something homemade, I needed something outstanding. At first, I was worried that my classmates would mumble something about the muffins being ‘too healthy’, but then I tasted them. They’re going to love them. I do!
    Thanks for the recipe and everything else, Natalie.

  10. Hey Sally!
    Can you replace the 1/3 flax seed with oatmeal?? Thanks!

    1. You can use 1/3 cup oats instead of the ground flax.

  11. These are fantastic! I made them with just 1/2 cup raw honey instead of sugar and a banana instead of the applesauce and they are plenty sweet! My two kids really enjoy them (score), I will be making these again!

  12. Made these this weekend. The muffins are really yummy and the recipe seems pretty forgiving! I made them as written, but suspect the batter would be easily customized. The muffins are really moist, but not in the gummy or tacky way muffins can be sometimes. Thank you Sally! 🙂

  13. These are the only thing my daughter will eat before Kindergarten!! So delicious, I feel like I’m cheating and eating dessert. I subbed out the brown sugar for coconut sugar and it worked great!

    1. I just tried these with coconut sugar the other day. SO fantastic, I agree!

  14. I made these muffins last night- amazing recipe! Just what I was looking for, something that I could throw a bunch of healthy things into and would still be delicious. I followed the recipe exactly. My only note, and if its even possible, I found them too moist and so I’d put in much less oil next time. 

  15. These muffins were a huge hit. My 11 year old son is so picky, but he loved them. I tweeked things a little, i did 1 cup of flour and 1 cup of oats. Added chia seeds and flax. My daughter, 9, not as picky as her brother, lite up like a Christmas tree when she realized there was chocolate chips inside. Very happy with these and will be making again. I actually got 24 muffins out of this receipt. Thank you for sharing this! 

  16. I just worked out points for these on the new weight watchers “smart points”
    Worked out at about 6points a muffin with the brands I used (I also did 1/2 plain flour 1/2 wholemeal) 

  17. Little bit late with the comments but you have no idea how awesome it is that you list out substitutes for this recipe! This separates you from many bakers I follow on my RSS feed! Thank you! 

  18. Love these muffins!!!! I made them using a few of your alterations (all brown sugar, all oil instead of the honey and applesauce) and did half golden raisins half dried cranberries. YUM! Also extra orange zest because I got a little excited while zesting my orange and couldn’t bring myself to throw the extra away haha. Can’t believe someone said the orange flavor was over powering though, it’s not a strong favour in mine and like I said I added over twice the amount of zest! 

    I do agree with one other poster though, these aren’t exactly simple. Lots of steps to get to the finished product! Which I’m fine with, the title is just a bit misleading. 

    Overall LOVE!!

  19. Will it taste alright if mango or mango juice is added?

    1. I’m sure they will. I would chop up the mango nice and fine and use it instead of the apple. And the juice instead of the orange juice.

  20. These look delicious and I’m planning on making them later in the week. If I were to use zucchini not instead of carrots would you suggest draining the excess liquid from the zucchini or leaving them as is?

    1. I’d maybe drain *some* of the liquid before adding to the batter. Let me know how you like them.

  21. These are delicious! I made them with 1/3 cup of mashed banana as a substitute for the oil and they are still moist and not rubbery at all! I didn’t have apple or crushed pineapple, so I made these with 1 1/2 cups of grated carrot and 1/2 cup of frozen unthawed blueberries. I also used aluminium foil cupcake liners to avoid sticking. We can’t stop eating them!! 

  22. I made these delicious muffins two days ago and stored them in an air-tight container. I used shredded carrots and the carrots are dark in color. The muffins are still moist & taste delicious. Has anyone else noticed the carrots being dark.

  23. I’m about to try this recipe, it sounds amazing! How do you recommend we do the oven heat and timing if I were to make mini muffins instead? Thanks!

    1. 350F for about 12-13 minutes 🙂

  24. I made just made these. I only had a cup of whole wheat flour left, and of course was feeling lazy about running to the store, so I used some of the pamela’s gluten free pancake mix (essentially a mix of rice flour, almond meal and potato starch). I otherwise followed the recipe, oven timing and all. These still came out super tasty.

    Thanks Sally for sharing. I’m looking forward to making these 100% the right way 🙂

  25. Made these puppies today.  Followed the recipe to the “T” as I do whenever embarking on a muffin journey.  I baked them in a large format six muffin pan with liners.  I went with with the Flax meal, orange juice and coconut oil which the author provided for choice.  I baked according to instructions, but went with 7 minutes at 425degrees before bumping down to 350 due to the large format.  Also needed about 26 minutes at the 350 temp to achieve al dente (ha ha).  Suffice to say they were delicious.  This is an excellent recipe for a healthy morning muffin.  I had one with freshly brewed pour over French roast.  As Phil Rizutto used to say, “Holy cow!” 

  26. Can I replace the juice with milk? I don’t have juice at home. Thanks in advance 🙂

    1. Milk would be ok!

  27. Sally, help! Due to the fact that I have two toddlers in my kitchen with me, I forgot to turn my muffins from 425 to 350, and so they spent 21 total minutes instead of five at 425! I tried one, and the inside still seems moist and flavorful, but the outside is a little crispy.  Do you think I can remedy this with some of your cream cheese frosting?  

    1. I’d say so! Everything can be fixed with cream cheese frosting 😉

  28. Susan Radford says:

    These are fabulous! The only alterations I made was adding chopped dried apricots instead of raisins (was out) , but threw. In some cranberries as well ! Delicious! Yea for cream cheese frosting too! Thanks Sally , love your recipes!

  29. I just made these and followed the recipe as is except I had to sub apple juice for the orange or pineapple juice because that’s all I had. I made 12 regular sized and 12 mini muffins with this recipe and they came out great! My 2 year old loves them!!! He’s had like 3 today which is probably more vegetables than he eats in a week lol. If anyone is curious I baked the mini muffins for 5 min at 425 then they took 10 more minutes at 350. 

    1. So glad both you and your little one liked them! Thanks for the timing of the mini muffins 🙂

  30. What a wonderful recipe! I’ve just made these little guys with additional banana and chia and they turned out light and fluffy and smell divine! Thank you for another great recipe Sally. This is the third recipe l’ve followed from you and your measurements, baking temperatures and baking times are always accurate. Thank you for your reliability and attention to details. Greetings from Cologne, Germany

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