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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. They turned out really well! I filled them 2/3rds full and was able to get 24 out of this recipe. They rose nicely and we’re better toddler sized for us. Thank you so much for including the weights in your recipe. There are a lot of ingredients but with a kitchen scale it goes pretty quickly.

  2. I haven’t made these yet, but if they are anything like your other recipes, they will be added to my “addiction” list. Don’t know who taught you how to bake, but you are a genius and often with minimal ingredients. Keep the recipes coming!

    1. Hi Cat! We would replace the applesauce with the same amount of mashed banana.

  3. So good! I used 1 1/2 cups ground oats, 1/2 cup whole oats and 1/2 cup buckwheat flour in place of the whole wheat flour. Didn’t use flax and substituted coconut sugar for brown and maple syrup for honey. Delish!!!

  4. Sally, great muffins! I’m trying to copy a morning glory that my mother in-law has purchased but can no longer find. Her 80th birthday is coming up and I want to surprise her with the muffins. I made the first batch and they were close. I’m trying to make them darker and a little more dense. I’m thinking about substituting butter for oil. any thoughts? Thanks

    1. Hi Jon, Melted butter will work! See the section in the post above called “Ingredient Variations/Substitutions” for all of the substitutes we have tested.

  5. A local bakery makes the best morning glory muffins that I have not been able to mimic until now! My doctor will be so thrilled because I make these with monk fruit instead of sugar and it helps to keep my blood sugars down. I also throw in dried currants, tart cherries, sunflower seeds and pumpkin seeds. I increase the cinnamon and ginger a titch and use a few drops of orange essential oil in place of zest. Lastly, I take a small amount of cream cheese frosting, add a couple drops of orange essential oil and then heat a little in the microwave until it is runny. Once the muffins have cooled, I drizzle a little of that yummy frosting on top—just to make them pretty.

    I use the large Paper Chef parchment lotus cups and my muffins look like they came from a bakery!

      1. It’s a straight across trade, 1:1 with sugar. I use the Lakanta brand.

  6. This muffin was very tasty and my husband, 6, 5, and 1 year old loved them! Yes it takes a lot of times to make and several ingredients so make a full batch, maybe two if you mixer can handle that much batter. I used crushed pineapple instead of grated apple and unsweetened coconut instead of pecan just because that’s what I had.

  7. Just made them! This is the second recipe I make from you and it’s truly amazing. I left out the pecans by accident I’m eating them on the side lol but I followed thru with everything else, soooo goodd!!

  8. I love the concept, (most) ingredients & the texture. However, the flax was over-powering. I will definitely make these again, but will leave out the optional flax this time. Any substitutions you’d recommend? Would wheat germ add similar nutritional content?

    1. Hi Ann, We haven’t tested these muffins with wheat germ, but let us know if you give it a try!

  9. Hi Jenny, 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. Another awesome recipe from Sally. I used ingredients I had on hand and added zucchini and they turned out amazing!

  11. These are the Best! I’m baking 4 dozen a week for 3 households. I started baking late in life ( during pandemic), your instructions/ substitution easy to follow..Thank-You!

  12. I’m not much of a cook but I can follow directions ‍♀️ Is it possible to use Almond Flour as a replacement Flour because of health issues I am not supposed to have Wheat. Thank you in advance because I would really love to make these. Regards, Cindy

    1. Hi Cindy,
      I haven’t made these muffins yet but like you, I cannot have any wheat. I’m planning on making this recipe using my own gluten free flour blend for cakes and muffins. For every two cups (250 ml, I don’t have a kitchen scale yet) I use 1/4 cup gluten free arrowroot flour, 1/2 cup gluten free brown rice flour and 1 1/4 cups gluten free sorghum flour. Sift all ingredients into a bowl and mix well before using in recipe. Free of xantum gum and has served me well for recipes with eggs or flax eggs. I hope that helps and you can make these muffins!

  13. Love this recipe! I was looking for something somewhat healthful but not muffins that made me feel virtuous for having made them while ultimately being inedible. I’ve made this recipe twice now with only 2 changes. I swapped out chia seeds for the flax meal and eliminated the honey entirely, using the brown sugar as the only sweetener. Also because I didn’t want to use a second muffin tin I spooned the entire batch into one 12 cup muffin it. That worked perfectly both times.

  14. Hi sally,

    can i use something else in place of eggs here.Normally i use applesauce to replace egss,but here its already an added ingredient.Can i use greek yogurt.

    1. Hi Artika, 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!

    2. 3 tablespoons of water mixed with 1 tablespoon of flax meal = 1 vegan egg

  15. Delicious! These muffins came out so moist, I was very impressed. I didn’t add nuts or raisins and substituted apple with pineapple.

  16. I’ve just eaten my first warm muffin and am restraining myself from eating a second. I used mostly red fife flour, with a half cup white flour. Coconut oil, raisins and craisins, pepitas and pecans. Added a bit of diced mango to the apple – carrot mix as it needed to be used up. Probably about 2/3 of the sugar -honey as called for. Some of these are going to my mom for Mother’s Day, so I appreciate the healthy ingredients on her behalf. It made 15 normal sized muffins. A bit of effort, with the grating, and lots of ingredients but well worth it.

  17. Last night, I got a hankering to bake some muffins, and found this one online. Because I hadn’t planned on baking, I wasn’t prepared with all of the many ingredients, so I made some substitutions and realized just how wonderfully forgiving this recipe is!

    Specifically, I used regular AP flour (not whole wheat), macadamia nut milk (not OJ), 1/2 cup of mango-peach applesauce (not 1/3 cup unsweetened applesauce) with the remainder of the 2/3 cup (applesauce + oil measurement) being avocado oil, dried orange rind (not fresh zest), slivered almonds (not pecans), and a little more than 1 cup of dried fruit — blueberries + cranberries + golden raisins — (not 1/2 cup regular raisins).

    I also added some flaked coconut, extra vanilla extract, some orange extract, and right before popping the muffins in the oven, I sprinkled the tops with toasted green pepitas.

    Finally, I used a 6-hole large muffin tin, and between 2 batches, I ended up with 10 muffins.

    I followed the baking directions to the letter, and the muffins were absolutely perfect! Golden brown, moist, with great flavor and texture. I will pass this recipe along to friends and family, because it’s a keeper!

    1. Hi Irene, 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.

      1. As I stated in my review above, I used a large 6-hole muffin tin and followed the recipe to the letter when it came to baking time…. 425°F for 5 minutes, then 350°F for another 18 minutes. If I’d continued to bake them beyond the 18 minutes, they would have been too dry.

  18. Love these muffins! I put my own spin on your version adding coconut, fresh pineapple, variety of juicy exotic raisins etc. Ive tried different MG muffins but this recipe is the best!
    Reminds me of one of my favorite coffee places in Salida,CO they also make a great MG muffin. Bravo! I also just made a batch using powdered Chia seed instead of flax since that is what I had on hand. Your site is my go to for fabulous recipes! Thank you! Family, friends, co-workers, husband appreciate all of your shared wonderful recipes. : )

  19. I love these muffins and make sure I always have a few in the freezer for a quick breakfast or a fast snack. Confession … I add a 1/2 cup of dark chocolate chips to the recipe. … I call them “Glorious Morning Muffins.”
    Thank you for sharing this recipe. SO GOOD!

    1. Hi Henriette! 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:

  20. Great recipe! I use the “Pulp leftovers from my morning veggie and fruit juicer. And add a little coconut and gf flour. My whole family loves them! Thanks!

  21. Can pre-shredded carrots work? Or does the liquid from the fresh grated add to the moisture content?

    1. Hi Nicole! Pre shredded carrots are dry so we don’t recommend using them. Best to stick with freshly shredded!

  22. These turned out to be the best muffins Ive baked so far! I replaced applesauce with 3% yogurt , and made a cream cheese frosting and I am in heaven !!

  23. I made these today in jumbo form, using your Master Bakery-Style Muffin cook temps/times and they are a DREAM! Topped them with raw turbinado sugar and sesame seeds.

  24. These are delicious sally made them 3 times already. I substituted the apple sauce for melted butter,the honey for more brown sugar and the apples with shredded cucumbers. Definitely a keeper recipe

  25. I loved these with the carrot & apples as mentioned but would like to add a can of crushed pineapple instead this time. Do I drain the pineapple & use the juice instead of orange juice? How do I substitute in for the apples &/or applesauce?

    1. Hi Maureen! You can use drained, crushed pineapple in the place of the applesauce or shredded apples. See the section of the blog post titled “Ingredient Variations/Substitutions” for details on using pineapple in these muffins. Enjoy!

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