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


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)7. 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. 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

Hands down, one of my favorite muffin recipes! Freezer friendly, wholesome, healthy, and EASY morning glory muffins!
This wholesome muffin has it all! The flavor of these morning glory muffins is incredible and they're super moist.


  1. Thank you for the wonderful breakfast idea! Made these today. I substituted one chopped juicy kiwi for raisins and orange juice. Muffins turned out delicious, but were reeeeeeally sticking to the liners 🙁 I wonder if that’s because of the substitutions I made?

      1. Good thought! I’d never had the need to spray liners before, but I’ll try it next time I make these goodies 🙂 Happy Easter!

  2. These muffins sound like what *I* think fruitcake should be…packed with real fruits/vegetables, not candied, alcohol-soaked madness 😉 And so much room for variation, as you noted! I’d like to try a tropical version with dried mango pieces, coconut, maybe pineapple juice instead of orange… 😀 Happy Easter, Sally!

  3. I love anything carrot cake right now, so I have a rumbling tummy on this sunny (!!!) Easter morning! By the way, soaking raisins has to be the smallest & best tip for any goodie with them. I despise hard-as-a-rock raisins!!! Plus, you can soak them in rum, too 😉 Happy Easter, Sally Kevin && Jude!

  4. Ha ha!! Love the demented Easter bunny link!! Too damn funny,,,and creepy! I’m gonna hop outta bed, maybe, and bake something now! These kind of remind me of my moms old Jamican jungle bread,,, that is sooo good too. Happy Easter and good luck with your new cookbook!

    1. To keep the same rich, moist texture in these hearty muffins– I’m unsure. Let me know if you try anything.

  5. Happy Easter! These muffins look great. They are my favorite because they are sweet and treat like for a special breakfast but also packed full of goodness. Great way to start the day!

  6. I can’t imagine anything better than having a dessert for breakfast .. especially when it’s Easter! 🙂

  7. First-time commenter! Saw this recipe right when I woke up this morning and it’s exactly what I’ve been looking for for the last few weeks. Bought some raisins at Trader Joe’s, had everything else and they just came out of the oven – delicious! I used a combination of white flour, almond flour, wheat germ, and flaxseed meal to make up the 2 cups of flour, followed all the other directions. I didn’t measure things exactly (especially the carrots and apples), so it seems to be forgiving. Thank you! 🙂

  8. Applesauce question! We don’t really get commercial applesauce over here (unless it’s puree for babies, or for eating with roast pork), so how would you advise making it? Much obliged.

    1. Hi Nicola! I’m sure you could use the applesauce you are referring to. You can also use the alternative suggestions in the recipe notes.

  9. Morning Glory/Glorious Morning muffins are my best seller where I bake in Northern Virgina! Where did you stay at? There’s so many wonderful places, Marriott Ranch being my absolute favorite (a little biased on that though). Loved reading your rendition of these!

  10. Is there possibly a substitute for the orange/pineapple juice? I have all the other ingredients and I’m so ready to try these, they sound delicious and still healthier!

  11. These would be a great way to start any day, Sally!! A carrot cake / apple cinnamon muffin hybrid sounds right up my alley. I hope you and Kevin had a wonderful Easter. That picture of Jude with the rabbit ears is adorable!

  12. What a cute bed and breakfast! It definitely looks like a nice place to relax 🙂
    Morning glory muffins are a favorite! Have to make these for breakfast (or anytime, for that matter!)

    1. I calculated with MyFitnessPal, but keep in mind I put the exact brands of the ingredients I used- so for you the values might be a bit higher or lower.
      Also, I didn’t use any substitutions and made the recipe as suggested (ingredients and amounts both).

      Per muffin:
      205 calories
      9g fat
      29g carbs (out of which 16g sugar)
      5g protein

  13. Wow! These do look amazing and chocked full on nutrition! Great way to start the day!

  14. I made this on the morning of a school trip. A real quick, easy, and delicious recipe. This is going to my favourite.

  15. Don’t you just love the food from Bed and Breakfast places. I guess if the type of business you have actually lists a meal it better be good.
    I used to make a muffin like this years ago. Forgot all about it. I’ll have to make this version. Thanx!

  16. These sound like the perfect breakfast treat! I’ve never tried a Morning Glory muffin, but these look great!

  17. These muffins look SO yummy! Muffins for breakfast – one of the best things ever. I love that you can grab and go!

  18. So, so, so YUMMY!! 🙂 I love all the different mix-ins–the more the better! Morning Glory muffins are like a breakfast party in your mouth! Can’t wait to try these!

  19. Thanks for putting the temperature in celsius Sally! I always had to calculate it, google is my life saver 😉

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