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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. I substituted chia seeds for the flax, because that’s what I had. They are so good. My family loves them.

  2. Absolutely delicious ! I used 1/4 cup of brown sugar and replaced 2 out of the 3 eggs with chia seeds (1 tablespoon chia seeds with 3 tablespoons of water to replace one egg). I baked them at the temperature recommended and they came out high and perfect. This is a recipe keeper ! Thank you !

  3. I have been using the Cooks Country recipe for my Morning Glory muffins but will be using this recipe going forward. It’s a very versatile recipe that can be altered in many ways to meet your desire. I wanted a muffin that would be my pre-workout breakfast with my morning coffee, so I added a large scoop of vanilla protein powder and to give them added moisture, I added one 5oz. Chobani vanilla Greek yogurt and 1/2 cup shredded coconut. To add more fiber I added a 1/2 cup of ground(in blender) high fiber cereal like, Ezekiel Golden Flax. Muffins turned out moist and delicious. What really stood out in the taste was the coconut and mini chocolate chips. One of my best. The other recipe calls for adding pineapple with the juice, but after adding the orange juice, i didn’t miss the pineapple. Very glad I found this recipe.

    Thank you

  4. Made this this week after getting too many carrots in my CSA box. Used pineapple juice instead of the OJ (we had some open) and they were great. Ate some as healthy snacks and we put cream cheese frosting on some and ate as cupcakes after dinner as well.

  5. Absolutely love this recipe. Have passed onto both my daughters. Tried with and without bannana, prefer with. Used MCT liquid coconut oil. Added chopped dried apricots and cranberries. Threw a whole peeled orange into food processor instead of just orange juice. Thanks for this yummy healthy recipe.

  6. I made these muffins for the first time today. I did substitute gluten free flour (Bob’s Red Mill 1 to 1 Baking flour is my usual) and as I read in the comments, I soaked the raisins prior to mixing them in. Muffins came out beautiful, moist, and delicious!

  7. Can I use both ground flax and flax seeds? I already added the flax seeds but I’m wondering if it’s okay for me to add both? Or just stick to the seeds?

    1. Hi Julia, we haven’t tested the recipe with flax seeds in addition to ground flax. For best results, we recommend sticking to the recipe but let us know if you test anything.

  8. Fantastic recipe! Easy and delicious! I used dried cranberries and no nuts or orange zest (didn’t have any) but otherwise followed the recipe exactly and they turned out perfect (I managed to get 18 total). I did the nutrition math (for my 18 muffins based on what I used) and for anyone who wants to know, these are only about 150 calories each 🙂 Baked good lovers rejoice!

  9. Just delicious morning pop…not to forget a delight snack! Followed recipe except used whole Chia seed(had no flax)…
    Made 14 muffins and we are ready for another batch!

  10. At first everything turned out great, I made mini muffins. I did not include the flax and instead of apple, I added more carrot.
    After sitting on the counter for an hour they have all turned green. Are these still safe do eat? Any idea why they turned green?

    1. Hi Megan! This is usually a reaction from the baking soda and shredded carrots– give it a quick internet search. It’s normal! And they’re still totally edible.

  11. I tried this recipe and it turned out very nice but the muffins were dry. Any thoughts on this are appreciated! Thank you.

    1. Hi Tony, Did you make any ingredient substitutions or changes? There are plenty of wet ingredients in this batter as written to keep them moist. Make sure you are measuring your flour correctly (spoon and level, not scoop). Also it’s possible that the muffins were over baked. If you try them again try checking them earlier.

      1. Thanks for the tips! I will try these suggestions.

  12. I’m looking forward to trying this! Could these be adapted to jumbo muffins?

    1. Sure can, Niki! 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.

  13. this recipe was a win for my picky toddler!! I used zucchini and carrot instead of apple. I omitted 1 egg for 2 bananas, used Greek yogurt instead of the orange juice and coconut sugar instead of the brown sugar. We also added about 1/4 cup chocolate chips and shredded coconut. Delish!!

  14. Without the flax ( I didn’t have any), to make 16 muffins, total calories was 181 per muffin. 6 grams fat. Thanks!

  15. Wow these are amazing! I love the flavor! I used apples (1/2 cup) , carrots (1 1/2 cups) and crushed pineapple (2/3 cup), maple syrup, orange zest and juice, cranberries and pumpkin seeds (so good). I made them as jumbo muffins. I love all the different ways that we can make these. Thanks so much for posting, I will be making them again soon!

    1. Shannon, I was going to make these tonight and was wondering about baking time for jumbo muffins – how did you adjust for the larger size? Thanks in advance!

  16. Hi Lisa, I just saw this. I thought that there would be some adjustments for this or even additional pans needed but I was able to make them in one jumbo 6 count muffin tin. I baked them at 425 for 5 minutes as Sally directs in other jumbo muffins and then 350 for 25 minutes or until toothpick test is clean. Oh and I used parchment paper as the liners.

  17. Great recipe!
    I used about an inch of fresh grated ginger instead of powder; every so often you get a little ‘hit’ of ginger rather than a background warmth. The next variant is going to be adding some jumbo oats (they’re healthy, right?) – maybe just as a streusel-type topping – we’ll see.

    1. I’m not a big ginger fan so I used Chinese 5 spice blend ( Anise, Cinnamon, Star Anise, Clove, and Ginger). A friend turned me on to it, I’ve been using it in everything. Adds “spicy-sweet” to Chinese, roasted meats, and cookies, and cakes.

  18. Baked these for 23-24 mins at 180 after baking at 220 for 5 mins in a small halogen oven. Followed the recipe with a few alterations and substitutes like walnuts for pecans and dates for raisins from my leftovers in the house. Cut down on the sugar because my partner hardly eats sweet food. Took a while to prep because I also made the applesauce from scratch, but worth it. Turned out great for a novice baker. Loved the taste and the variety of ingredients. Easy to follow and only using simple baking tools. Thanks for sharing the recipe and your tips.

  19. I made these as a way to get extra veggies veggies into my toddler and they are a huge hit! She’s currently eating her 2nd one for lunch (as am I) and I’m so impressed with their texture and taste. I was unsure about the whole wheat flour because, in the past, it has often yielded a too dense texture to taste like a real muffin (those tasted like “healthy” muffins). These muffins taste and feel proper, even with the whole wheat flour, and the raisins are a huge plus. I don’t like pecans so I did 1 cup of raisins to make up for no nuts and it’s a delicious outcome! Also, I used melted butter instead of oil because I prefer it and my toddler tries to eat straight butter so I’m trying to make sure she gets plenty of it in/on things instead of eating it from the stick. The orange vest and juice definitely heightens the flavours

    Thanks for a delicious muffin recipe!

  20. I accidentally made these vegetarian by forgetting to mix in the eggs! I’ll try making it again later with eggs, but these were still tasty! My husband and I happily ate them all.

  21. Hi I made these for first time yest and they are so delicious. Do you think this recipe would work in a cake tin or loaf pan?

    1. Definitely! I’m unsure of the best bake time, but use a toothpick to check for doneness.

  22. I made these today with all zucchini, no nuts and no raisins. I used tomato juice leftover from canning instead of orange juice. They are moist and tasty! And I’ve been using my food processor’s shredding blade instead of a box grater to process so much zucchini we’ve been given. I was worried the pieces would be too big, but they aren’t! I’ve made four different kinds of baked goods with this method, and it’s been perfect in each one. I love the adaptability of this recipe and all the options for subbing with what I have on hand.

  23. Spectacular! These were a perfect treat for the autumn equinox – spicy and warm. YUM! Thank you so much!

  24. Just made these and they are SO good! I love a healthier muffin. I pretty much stuck to the recipe except I only had white flour not whole wheat. Highly recommend.

  25. Amazing! Super healthy, not too sweet and my toddler and husband loved them. I love the hint of orange too

  26. This recipe is fantastic and I’ve made it many times since discovering it. Thanks for sharing! Would it be possible to make this as a bread? If so, what changes would be necessary.

    1. Hi Alexis, Yes! You can bake this in a 9×5 loaf pan without making any changes to the recipe. I’m unsure of the best bake time, but use a toothpick to check for doneness.

  27. Absolutely delicious! I grew up eating morning glory muffins from a bakery and these blew them out of the water. They are super moist and the perfect combination between sweet, tasty, and healthy. The spongy texture is amazing. I followed the recipe closely, using freshly made applesauce since I didn’t have any canned, fresh squeezed orange juice, and coconut oil. I baked them for 5 mins at 425 and 16 mins at 350, and that may have added to the moistness.

  28. These muffins are wonderful! Because my husband and I must live low-sodium, I am experimenting with salt hacks in my baking. It’s easy to halve or quarter the salt, but baking soda is a challenge—1200 mg sodium per tsp but necessary for leavening. For this recipe I reduced the soda to 1 and1/2 tsp, beat the eggs a few mins to incorporate air before slowly adding liquids, and used half white flour (to rise more easily). Worked beautifully! Thanks for a great and adaptable treat.

  29. Great recipe! I havent actually taken them out of the oven yet, but I had so much fun playing around with substitutions (I felt like a real baker lol). Thank you Sally!

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