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

  2. 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!

  3. 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.

    1. Thank you Shannon! I ended up not getting to these last night so tonight it is!

      1. Yay! You are welcome.

  4. 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.

  5. 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.

    1. Hey. Tried this recipe exact. However even after about 45 mins of bake time, the toothpick never came out clean. On trying one of the muffins, the taste was good and it did not taste raw or chewy, but it was still wet from inside all the same. All this moisture from the apples I guess. Is this normal or did I make any mistake?

      1. Stephanie @ Sally's Baking Addiction says:

        Hi Swati, Usually the total time these muffins take in the oven is about 23-24 minutes. Did you start your oven off at the higher temperature? Did you make any ingredient substitutions or different amounts? Next time if they aren’t baking through you can cover the pan with aluminum foil to keep the tops from getting too brown while the center bakes through.

  6. Lorraine Hebberd says:

    These muffins are delish, I just added coconut and chia seeds thanks

  7. 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!

  8. Wonderful recipe…only changed flour to 1 cup all purpose and 1 cup whole wheat…worth the time!!!Delicious

  9. 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.

  10. 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. Stephanie @ Sally's Baking Addiction says:

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

  11. 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.

  12. JULIE TIJERINA says:

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

  13. 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.

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

  15. 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. Stephanie @ Sally's Baking Addiction says:

      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.

  16. 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.

  17. 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.

  18. 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!

  19. Hi! Can this recipe be used for Jumbo muffins?

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Mandy, 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.

  20. Weird question: do you need to peel the apple before grating?

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Katie, Yes you can peel and then shred your apple. We hope you enjoy these muffins!

  21. Excellent. Used mashed banana instead of applesauce (thank-you for that option), added half a cup of chopped fresh cranberries, omitted the pecans and sprinkled a few salted pumpkin seeds on top instead.

  22. Absolutely delicious! Wouldn’t change a thing . I’m not a fan of whole wheat as the things I make with whole wheat tend to come out dryer and dense — but not so with this recipe. I have made these as mini- muffins several times and it has never failed me – super moist, fluffy and super delicious. I have been meaning to try freezing a batch for later, but they’re gobbled up by the kids (with a little help from me) each time. Thanks for a great healthy little snack/treat! – Wonderful recipe — it’s a keeper !

    1. Did you use the same temperature and cooking time with the mini muffin pan?

      1. Stephanie @ Sally's Baking Addiction says:

        For mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.

  23. Thank you so much for this wonderful recipe. Morning glory are my favorite muffins and I have been looking for a “healthier” version for a while. I made some substitutions based on preference and what I had on hand. Wheat germ for flax, 1 cup zucchini for 1 cup of the carrots, and 1/2 cup yogurt for the applesauce and honey, as I suspected the recipe was a little sweet for my taste. I also added shredded coconut. I especially like the fluffy texture and the domed top. This is my first recipe from this site but I will be back.

  24. Thanks for this amazing recipe! I didnt have enough carrots for the double recipe so I did 3 cups carrots and 3 cups apple. Didn’t have applesauce so I substituted Pumpkin purée and added 2 tsp pumpkin spice instead of the extra cinnamon. I didnt have flax seed so I substituted large rolled oats. The batter seemed a bit too wet so I added in 1 cup of large rolled oats in hopes that it will soak up some of the moisture. These are so tasty! So much flavour and texture. I will definitely be making these again!

  25. I substituted the flour for buckwheat flour. This recipe turned out beautifully!! <3 <3 <3. Thank you sooo much for the recipe. You are definitely a gifted baker!

  26. Just made these muffins and they are delicious. I cut the brown sugar only by a couple tbsp or so and they were plenty sweet for us! Next time I’ll add unsweetened shredded coconut for that extra chewy factor. 😉 I will also shred the apple instead of chopping it. Recommended cooking time was spot on.

  27. Hi
    This looks like another winner. Just a small query. By ground ginger do you mean ginger powder or grated ginger? How do you make pumpkin puree at home?
    Thanks for sharing your recipes.

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Rekha, Yes ginger powder that is sold in the dry spice section of the store. ther readers have reported making fresh pumpkin puree this way:

  28. Hello. I haven’t made these yet but excited to try them. I love the diversity of substitutions everyone has tried! Im allergic to nuts and apples, so this recipe definitely helps me! Has anyone tried using pear? I’m not great at substituting ingredients like pear for apple. Not allergic to those!

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Jane, We have not made these with pear but yes, you certainly can. Let us know if you try them!

  29. Followed recipe exactly, I’m an experienced baker, but at 19 minutes for the second step these were over-done. Too dark, dry. Disappointed. I have a convection oven but maybe I needed to shorten the first step at the hotter temp in addition to the second step.

  30. Sometimes I wonder why I even have a Pinterest account. I always end up choosing the Sally’s Baking Addiction recipe! I should just start here! Can’t wait to make these!

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