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. Didn’t have time or patience to grate apples, just diced them up. It added a wonderful texture, will continue to dice them instead of grating. Also added a bit of shredded coconut, just because. Absolutely my best batch ever, and I’ve made A LOT of batches!

  2. I never leave ratings but this recipe is so amazing I felt compelled to do so. Great balance, not too sweet, not full of oil/butter but still super moist, tons of flavor. Used coconut oil and threw in the shredded coconut as suggested. LOVE. Thank you, Sally!

  3. Made these with all whole wheat flour for a church bake sale. Wasn’t thrilled with the consistency due to the wheat flour, but two ppl that bought some raved, one saying he’d buy me a drink if I made him a whole batch, lol! Happy that I could do something nice, I made some tonight, subbing in 1 cup white all purpose flour for one of the whole wheat cups. Still healthy, but I love the taste and consistency even more!

  4. These are very good, Sally! I first saw these on your blog a few years ago and they’ve been on my list for that long. I finally baked them last night and we’ve already enjoyed half the batch! Thank you for your recipes. This one is a keeper.

  5. These muffins are awesome. Great hit at the office new year’s eve party!

  6. This sounds super yummy! Can I substitute almond flour instead? What do you think would be the equivalent? Thanks! 🙂

    1. Hi Jenna! The muffins will be too wet with almond flour. Instead, I recommend my blueberry almond power muffins.

  7. Absolutely love your recipes! I’d like to add oats in this. Do I soak it in milk like with your oat and blueberry muffin? Do I less use flour then?

    1. Hi Liz! That would require some testing. I’ve never added oats. If soaking, you’d have to reduce another wet ingredient. If using as dry, you’d have to *slightly* reduce the flour and/or flax. Let me know if try anything!

  8. Hi these muffins sound great however When I bake muffins I only want to use one muffin pan. The extra few muffins are annoying . Also 3 eggs . I notice a lot of your muffins require 2 pans for the extra muffins . ;(
    Maybe you can adapt for 12 or less muffins.
    Love your recipes !

    1. Thanks for sharing. Feel free to discard leftover batter or wait for the first batch to be finished to bake the rest.

    2. Why don’t you buy a dozen individual silicone muffin baking cups. Then you can fill with extra dough as you need, put on small baking tray (I use a metal pie plate) and bake them all at the same time. Works great!

  9. Sabra schroder says:

    Hi Sally, I’d like to turn these muffin ingredients into more of a lighter cake texture. Can you recommend what to add like baking powder or baking soda, etc? Thanks!

    1. Hi Sabra! I’m happy to help. I recommend leaving out the flax, swapping whole wheat flour for white flour, and reducing to 1 cup shredded carrot. (The wet ingredients can weigh it down.) You could probably also skip 1 egg and replace with 2 Tablespoons of milk, too. I haven’t tested any of this but this is where I would start. No need for extra leaveners.

      1. Sabra Schroder says:

        Will do Sally, thank you so much!!!

  10. I have tried your recipe with gluten free flour (Cup 4 Cup or Bob’s Red Mill); for me they have always turned out perfect. It’s so great to have a hearty GF muffin since most of them out there aren’t great tasting and/or very expensive to buy. Thanks for another (updated) great recipe!

    1. Thanks for letting me know that these muffins made with GF flour turned out wonderfully! I appreciate your positive feedback, Michelle!

  11. These look so good! I don’t have applesauce, so will need to substitute. If using mashed banana, would I need 1/3 cup? Or, if I were to use melted butter or oil – how much would I use? Thanks so much for all the amazing recipes you share. I’ve learned so much from your blog!

    1. Yes, 1/3 cup to replace the applesauce. It’s an even swap! Enjoy!

  12. Can I use white whole wheat flour?

    1. Sure can! Same amount.

  13. First time making these and first time ever leaving a review. I followed your exact recipe did not substitute or added anything else. Muffins came out delicious, perfectly moist and not too sweet.

    1. Thank you so much for taking time to leave a review, Diana! Thrilled you enjoyed these muffins 🙂

  14. Hi Sally

    Love all your recipes, every one I’ve tried is always a hit! Can’t wait to try this recipe!

    It may have already been answered but can I bake this exact recipe in a loaf tin or would some of the ingredients need to be edited?!

    Thank you!

    1. Hi Katy, Any muffin recipe yielding around 12 standard size muffins doubles as a quick bread recipe. You can certainly use this recipe and if you happen to have any extra batter you can make an extra few muffins 🙂 You can see my post on Blueberry Muffin Bread for my tips on turning muffins into quick breads.

  15. My insanely picky three year old called these “delicious” I am sooo thrilled.

  16. I made these yesterday to use up some extra fruits, veggies, and pantry ingredients. I love how versatile the recipe is and they are SO YUMMY! They may actually be better the next day. These are perfect for my super active husband, my busy toddler, and my snacky pregnant self. 🙂 Thanks Sally!

  17. DELISH! Easy to make and love your suggestions for substitutions! Family who I shared them with were very happy with their “Glorious Morning” muffin! Thanks Sally!

  18. Absolutely fantastic! Soft and tender, yet full of flavor.

  19. Hi Sally, made the Morning Glory Muffins, they are amazing. I prefer a dense muffin and these fit the bill, just the way I like them. Thank you so much for taking the time to post and share your recipes,. I love your site

  20. Hi Sally!
    A lot of the ingredients in the recipe are used as egg replacements, I would love to make a vegan version and I was wondering if you had any suggestions to replace the eggs or do you think it would be okay to just omit them completely?

    1. Hi Aisha! I haven’t tested anything. I wouldn’t leave them out completely, so feel free to add more wet ingredients, flax eggs, or anything you’ve successfully used as a vegan egg replacer in other muffin recipes. (I’m not a pro at vegan baking, sorry!)

  21. Thanks for updating this post, Sally – the new pictures have wonderful lighting and colour, love it!
    I made a halve recipe of these for my mealprep this week and got 9 muffins out of it. They taste great and keep well!
    My ingredients variation: whole grain spelt flour instead of whole wheat, shredded pear for part of the shredded carrot (didn’t have enough carrots… I used a very firm variety of pears, amazing addition!), walnuts for pecans, freshly squeezed tangerine juice instead of orange juice (didn’t have any oranges).

    1. I’m so glad you enjoyed this recipe, Sina! Your variations sound delicious 🙂

  22. I’d give 10 stars if I could. Sally, these are the BEST muffins I have ever had, from the texture, to the spices, to the subtle sweetness. These are definitely going to be a regular thing at my home from now on. Thank you so much for sharing!

  23. Love, love, love morning glory muffins. Thank you! This got me wondering. I made your baked oatmeal recipe – a huge hit with my family. Think there is a way to combine the two recipes – the flavors of morning glory muffins with baked oatmeal? Hmmm…

    1. Hi Jen! You can leave out the berries in the baked oatmeal and add shredded carrots and apples, along with some ground ginger (there’s cinnamon already there!) and raisins (and/or pecans), too. Delicious. Enjoy!

    2. Okay…let me say these are our favorite muffins!! Love how there are so many yummy textures going on! Thank you for this yummy recipe! I add flax seed, hemp, and chia seeds for that extra healthy kick!

  24. I only have pears on hand can I use that instead of grated apple?

    1. Absolutely!

  25. Absolutely DELICIOUS!! I’m on a new healthy lifestyle diet and these fit the bill perfectly!!

  26. These are delicious! I made them with dried cranberries instead of raisins and omitted the ground flax (just because I didn’t have any). The whole family loved them, including my 5 year old and 16 month old. I used an online recipe calorie counter, and with the modifications (cranberries instead of raisins and no ground flax seed), for a yield of 16 muffins, it came out to 218 calories per muffin, which is great!

  27. Margo Stretch says:

    I made these today, and have a question: I found with 2 tsp baking soda in them, there was a lingering taste from that which I didn’t prefer… I’m wondering if you know of any reason these wouldn’t work as well with both baking soda and baking powder, to lessen that soda-y taste. They’re a fairly involved recipe, so when I make them again, I want them to turn out well. I don’t want to sub in baking powder if there’s good reason to stick with the full amount of soda. What are your thoughts?

    1. Hi Margo! You can definitely play around with this recipe and use some baking powder to replace the baking soda. Just remember that baking soda is 4x stronger than baking powder. And depending how much you replace– I fear with that much extra baking powder, the bitter aftertaste would be quite pungent.

      1. Margo Stretch says:

        Thank you Sally. I will tweak it just a bit.

  28. hi Sally
    These look wonderful! Wanted to know if i can use Whole Wheat Pastry flour ??
    thank you!

    1. Hi Michele, Whole wheat pastry flour is lighter in texture and lower in both protein and gluten. I have not tested it so I’m unsure if pastry flour would hold up to the moisture in this batter. If you try it out please let me know!

      1. I used whole wheat pastry flour today and they turned out perfect! I also used it in place of whole wheat flour in your banana bread. I use it in most of my quick bread/muffin recipes – all good! I made your red velvet cake for my twins late birthday celebration yesterday. While I didn’t use enough food colouring to get that beautiful red shade, everyone loved it!

  29. I have small children, so we often make mini muffins. How would I change the cooking temperature/time to accommodate mini muffins? These were delicious!

    1. Hi Courtney, For mini muffins, bake for 11-13 minutes at 350°F (177°C) the entire time or until a toothpick inserted in the center comes out clean.

  30. These are so good! Well worth the tiny bit of extra effort to prepare the ingredients. They even got the thumbs up from my 6- and 4-year-olds. And don’t leave out the orange zest/juice if you can help it – such a great background flavor! Thank you for this recipe!

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