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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. So yummy! I didn’t have any applesauce on hand so I used greek yogurt instead. They turned out great!

  2. These were perfect. Moist ,sweet but not too sweet. I didn’t have orange zest so I used the zest of lemon which gave it a subtle yet bright kick. I also added a bit of cardamom just because. Lol. I enjoyed these. Thanks Sally

    1. Hi Beth, absolutely! 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.

      1. Can you omit the honey?.. and if you do should you sub something?

      2. Hi Gordon! See the section in the post above titled “Ingredient Variations/Substitutions” for details on substituting the honey. Enjoy!

  3. I added a cup of oatmeal instead of flax, pineapple instead of apple, 1 cup of coconut, 1 cup sliced almonds, and craisins instead of raisins.

    1. Hi Donna, absolutely. You may want to decrease the amount a bit, but that’s up to your personal preferences. Let us know how it goes!

  4. These muffins are so yummmm. I omitted the apple sauce., replaced the raisins with chopped dates.
    Couldn’t resist having one as soon as it was out of the oven! Broke it and spread a nice layer of butter on each half. Delish

    1. Hi Loretta, we haven’t tested these muffins with GF flours but please let us know if you do!

  5. How would I adjust the baking time if I wanted to use a large 6 count muffin pan?

  6. So versatile. I needed to make them GF so used 1/2 c almond flour, 1/2 c quinoa flour, 1/2 c. coconut flour, and 1/2 c. gf blend. First time made as directed otherwise–yummy! Second time didn’t have any applesauce, brown sugar, or apple, so used banana, coconut sugar, and zucchini–still yummy!

  7. These were delicious muffins. First time I made them I was not in my kitchen and forgot the baking soda…oops, hockey pucks! Second time, the next day, I made again with baking soda. Light, delicious, wonderful warm or cold! I also love all the possibilities for mix ins. The orange zest with craisins added a wonderfully bright kick!

    1. Hi Marg, for best results, we recommend making two separate batches rather than doubling.

  8. This recipe is amazing and I tweaked it a bit and it came out great. I used
    1-1 Gluten free flour, banana instead of applesauce and half of the cinnabar’s half pumpkin pie spice.
    Delizioso!!! Using this gluten free flour (Bob’s Red Mill) was great. It did not crack, crumble or come out dry at all. I was surprised.
    This recipe is a keeper. Enjoy baking ladies!!!

    1. Hi Allison, we recommend using a crisp variety of apple, not a mealy one, for best results. Tart apples we love to bake with: Granny Smith (in Sally’s opinion, this is the best overall apple for baking), Braeburn, Jonathan, and Pacific Rose. Sweet apples we love to bake with: Jazz, Pazazz, Honeycrisp, Pink Lady/Cripps Pink, and Fuji.

  9. So delicious!! I made them per the recipe adjusting the carrot to apple ratio to more 50/50 and added just a sprinkle of allspice and they were amazing. Thanks for another wonderful recipe!!

  10. I make these ALL THE TIME. today i didnt have applesause and used pureed sugar pumpkin (from my garden) and they turned out absolutely beautiful

    1. Hi Narusha, we haven’t tested this recipe with any egg replacements, but let us know if you give anything a try.

      1. The arrival of Autumn signals the perfect time for Morning Glory Muffins. I certainly make them year-round but they just look, smell, and taste like what Fall to the senses must be like.

        They do take a bit of prep time but the effort is so worth it.

        Great recipe, Sally!

  11. Hi Sally – Adore these muffins! Would love to add some canned pumpkin – how much would you recommend? Thank you!

    1. Hi Mil, So glad you love these! You can use canned pumpkin in place of the applesauce.

  12. If using all purpose flour, is it the same amount? And do any of the other ingredients need to be altered?

    1. Hi Carly, we don’t recommend freezing batter. Once the leaveners are added, they become activated and it’s best to bake the batter right away. You could, however, freeze the baked muffins. They thaw wonderfully and could be popped in the microwave for a few seconds for a warm muffin!

  13. I made these muffins with King Arthur gluten free flour, fresh lemon rind and lemon juice because I didn’t have oranges, I didn’t have the applesauce either and they tasted amazing. So delicious. I love carrot cake and they taste like carrot cake without the frosting.

    1. Hi Amanda, we like to individually wrap the muffins in Press N Seal (or any plastic wrap) and then store them in a storage bag or tupperware container for extra protection from moisture.

      1. What are best practices for thawing them and how long does it take?

  14. I love how you added alternatives for
    all of the ingredients! Very versatile. I will definitely make these again, maybe even replace my main muffin recipe.
    I subbed sweet potato for the applesauce and pineapple for the shredded apple.

  15. Absolutely delicious! I couldn’t resist eating one hot out of the oven . It was so good that I had a second with butter. Oh my gosh so incredibly yummy! Thanks for the wonderful recipe!

  16. This recipe made great muffins – sweet (without using oodles of sweetener), very moist and fluffy. The only thing I would tweak, is adding some more fillers – nuts, seeds, coconut – to make them a bit more robust and chewy.

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