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

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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. 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)

  2. 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.

  3. Can I bake this in a loaf pan? If so what would the cooking time be? Thanks Sally your recipes never fail me

    1. Trina @ Sally's Baking Addiction says:

      Hi Emily, 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.

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

  5. 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!

  6. 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).

  7. Can this recipe be used as a loaf? If so, how would I change the cooking time? Thank you

    1. Lexi @ Sally's Baking Addiction says:

      Hi Catherine, 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.

      1. Maybe I’ll give it a try next week as I did see your earlier response just missed it… I ended up making your oatmeal blueberry muffins and they turned out wonderfully. Made them a little more healthy by using it xylitol instead of the honey.

  8. 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!

  9. 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.

  10. 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.

  11. Idolka Salgueiro says:

    Sally, can I substitute the brown sugar for maple sugar or should I make it 185g of honey instead. Or just leave the brown sugar out completely? I’m trying to reduce my processed sugar intake.
    Thank you!

    1. Trina @ Sally's Baking Addiction says:

      Hi Idolka! Coconut sugar is a dry unrefined sugar you can use in its place.

  12. 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.

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

  14. Delicious! My fifth-grade son wanted two!

  15. Cindy Muhleman says:

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

  16. My son has an egg allergy will substitute the 3 eggs for 3 flax seed eggs; I’m hoping for success – I will let you know

    1. Annie did you make these using the flax eggs?? How did you make your flax eggs if so?? I can’t eat eggs either.

      1. Yes
        1Tbsp of flax seed meal to 3Tbsp of water
        For 3 eggs add 3 Tbsp flax seed meal (ground )and 9Tbsp of water mix in small bowl let sit for 10 minutes
        Add to recipe where it calls for the 3 eggs but do not add the flax seed that the recipe calls for if you are using eggs
        I used oj not pineapple
        I used canola oil but next time going to try coconut oil
        I also added coconut flakes
        These turned out wonderful
        Froze well
        They are wonderful warmed up w a cup of tea

  17. Hi sally, great recipe! Is it possible to add coconut?

    1. Lexi @ Sally's Baking Addiction says:

      Hi Christine, absolutely! See “Ingredient Variations / Substitutions” for more details.

  18. 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!

  19. Can you suggest baking time if I make them as mini muffins instead?

    1. Stephanie @ Sally's Baking Addiction says:

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

  20. Delicious, the best muffins I’ve ever made. Thank you

  21. Any thoughts on replacement for the egg in the recipe? Or maybe some of the egg?

    1. Lexi @ Sally's Baking Addiction says:

      Hi Laura, 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!

  22. 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.

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