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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

Description

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.


Ingredients

Scale
  • 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

Instructions

  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.

Notes

  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. Do you have any suggestions for how long it would take to bake these in a jumbo muffin pan?

    1. Hi Sarah! 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.

    2. I love this recipe. I used plantain flour and it was just great. 3/4 cup of plantain flour for 1 cup whole wheat flour.

  2. Sally,
    These muffins sound delicious. Have you tried baking this in a loaf pan instead of muffins?

    1. Hi Henrietta! 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.

    2. Start checking at 45 minutes in a fan oven or 50 minutes with no fan/gas oven. Or my favourite method is to check the cake 5 minutes after the cake smell comes through the room. I just baked 1/2 recipe of Sally’s carrot cake in an 8x5in loaf tin and a toothpick came out clean after 45 minutes using a fan oven, and that’s a moist batter like this one 🙂

  3. WOW, delicious! Only modifications I made were to sub mini chocolate chips for the pecans and used Trader Joe’s Golden Berry Blend (dried cranberries, blueberries, cherries and golden raisins) in place of all raisins.

  4. Fabulous recipe as always, Sally! Followed recipe exactly with following substutuons; melted butter for oil, crushed pineapple for applesauce, and AP flour for whole wheat. Used zest and juice from a mandarin and some reg OJ to make up diffetence. Next time I will increase orange zest a bit. Overall, this recipe is spot on and has a wonderful flavor, soft and fluffy texture, and bakes up perfectly. The bake temp and time came out beautifully! For those wanting a sweeter muffin, try adding a simple glaze of orange juice and powdered sugar. I think they are perfect without though. These are yummy enough for an after dinner treat but healthy enough for a quick breakfast for the kids or myself. Thank you for all the excellent recipes Sally! I am a long time fan and appreciate the time and detail you put into creating well thought out bakes.

      1. Would you happen to have any of the nutrients information such as calories, fat, fibre, protein etc (based on the base recipe)? Thanks

      2. Hi Nicole! We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076

  5. These are so good. I have to limit myself to 2 a day. I used everything that was in the recipe except the ground flax as I didn’t have any. Instead I used 1/3 c of rolled oats and added 1/2 c of coconut. They are a few days old but still so good. I will make them again and add pineapple and nutmeg. I look forward to experimenting with this recipe. Thank you Sally and group for this great recipe!

    1. Thanks for the modification advice. I cannot eat flax seed so I’m anxious to try with the rolled oats and coconut!

    1. Hi Heather, I’m unsure. That would require additional testing. If you try anything, let me know!

    2. I use Kodak for all my muffins but if I add a whole bunch of other good stuff I add baking powder and liquid if needed . I especially like adding the leftover juice from plumping my craisins in orange juice. Yummm.

  6. These are amazing! I was a bit worried about the number of ingredients but it was fine. I also love that they seem quite forgiving and you’re able to easily substitute. Ground flax isn’t that popular in the UK so I bought flax seed with the intention of grinding myself but they’re so shiny that just wasn’t happening so I threw them in whole and it was fine. Again, unsweetened apple sauce isn’t popular here either so I got a jar of apple baby food (100% apples) which I thought was good thinking if I do say so myself haha. I also used half cranberries, half raisins. All in all they turned out great! I baked them for slightly longer because my oven struggled to get back up to that high initial temp after I opened the door to put the muffins in, I just kept testing them with a tooth pick until clean as Sally recommended and they’re so moist and delicious. Another success thanks to Sally! Next week I’m going to make her whole meal banana muffins to use up the wholemeal flour I bought for this months baking challenge! Can’t wait.

    Note: I entered the ingredients into an app to get nutritional info out of interest. They worked out about 250 cals with lots and lots of goodies (bags of vit A, vit C).

    1. Hi Jody! We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076

  7. This recipe sounds great. Will them today. Planning to add some unsweetened shredded coconut. Yum!

  8. Tried these muffins today and they are befitting their names. Followed recipe to the letter…these are DELICIOUS!!!! Thank you.

  9. The muffins are delicious!
    I was wondering if I could bake this in a Bundt pan

    1. Hi Donna, we’ve never tested this recipe as a Bundt cake. It may be a bit short but it should work. You can also 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.

  10. Thank you for the recipe—I have loved absolutely everything I’ve made from this site (your 6″ cake info is a revelation!). This recipe is on my short list of things to bake, but I have a question about honey. I have a jar of creamed honey, which I’ve never baked with before. Do you have any experience with it? Would I need to adjust the amounts?

    1. Hi Kimberly, We haven’t personally tested it but it should work the same in recipes as regular honey. Let us know if you give it a try!

  11. So delicious!! I needed them GF, so I substituted 1 1/4 C GF AP flour (203 gr) , 1/4 C Teff & 1/2 C Buckwheat, for the ‘bran-wheat’ taste. I mounded the baking soda to account for the diff flours. They are so good, just like I remember! Thank you!

  12. These muffins are amazing!!
    Definitely worth the 5 WW points
    Love the website! Everything I try turns out fabulous! Love the directions and tips.
    Breakfast cookies next!!

  13. I just made these over the weekend and they were delicious and toddler granddaughter approved. Thanks for great, healthy recipe.

  14. Yum! Approved by everyone in my family (husband in the trades that needs fast substantial snacks, me always looking for delicious and healthier choices, and three teens).

    Love how easy it is to adjust/adapt to what I have on hand. This batch used half whole wheat/half ap flour, maple syrup for honey, pumpkin spice for ginger, pineapple juice (accidentally bought pineapple rings instead of crushed), dried cranberries instead of raisins, and lastly coconut in place of nuts for my picky eaters.

    Half of the batch got gobbled up as after school snack/dessert the first day. Rest were breakfast and packed in lunch boxes the next day. Next time will double recipe to freeze some for grab and go, crazy days!

  15. So good! I love the apple and carrot combination; I sometimes exchange the raisins for cranberries or mix them both. With the modifications it helps me a lot in case that i don’t have one fo the ingredients. They are just super delicious!!!!

  16. I used I/2 spelt flour and they were still light and moist! Great recipe, worth the effort for sure!

  17. Excellent recipe! Great classic flavor I was looking for. Of course….I did change a few things because of what I had on hand, still turned out really great.
    I skipped the egg, juice and applesauce – subbed with two bananas. Added the flax for egg replacement, binder, flavor and fiber.
    Added 1/4 tsp nutmeg because of the banana. I did add the orange zest! Flour was 1 cup buckwheat and 1 cup sprouted oats to make gluten free (for my daughter’s dietary restrictions). Lastly, used only coconut sugar instead of the sugar and honey, and avocado oil because it’s a nice neutral and healthy oil choice for muffins. Sounds like a lot of adjustments but same flavor is retained and am used to adjusting for food allergies. By default it’s vegan too, if needed.

  18. These muffins were moist and delicious, however, they all stuck to the muffin liners, especially on the bottom. I’ve made alot of muffins and never had this happen before. I omitted the flax, and used more apples and less carrots. I baked them 3 minutes less than the recipe states, and they were baked perfect. Any idea why they stuck on so much. Love your website, thank you!

    1. Hi Janice! Did you allow the muffins to fully cool? Warm muffins will usually stick to liners. Also make sure to use a high quality liner to avoid sticking in the future. Thank you so much for giving these muffins a try!

      1. Silicone muffin pans are the best! Prettier muffins without paper liners.

    1. Hi Raja, see blog post above: “If needed, replace with melted butter or more oil, apple butter, mashed banana, canned crushed pineapple, or pumpkin puree.

  19. Only just noticed the carrot says shredded but the apple says both shredded or grated, what’s the difference? I always used a box “grater” with the larger “shredding” function which is just confusing me more the think I about it haha

    1. No difference! Use your box grater for both – happy baking!

  20. Anyone tried adding fresh fruit such as blueberries to the batter? 150g/1 cup replacement for 150g grated/1 cup of veg?

    1. You can replace the raisins or pecans with the same amount of blueberries. Enjoy!

  21. Really good recipe.
    I made some changes only because of low pantry.
    Used all purpose flour.
    Used a can of crushed pineapple in lui of oil. ( fat free diet)
    Cranberries in Luis of raisins.
    Everything else stayed the same including cooking times. They are awesome.

  22. Hi, I love these muffins so much. They are my go to muffins. This time I was wondering if I could put maple syrup instead of honey?
    Thank you so much!

  23. LOVE this recipe. I have made it multiple times with different substitutions, however, the carrots keep turning green the second day. Is this because of the baking soda? What should I do?

  24. Well to my surprise these came out so rubbery and inedible…. well not quite but to me they were but my chickens enjoyed them What went wrong?

    1. Hi Sharon, thank you for trying this recipe. Did you make any recipe substitutions or leave out the oil by any chance?

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