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

More Healthful Baked Goods

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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 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


  1. First time on your blog. Great muffin recipe. Love all the variations. I did a few subs: 1/4 c maple syrup for honey, reduced pecans to 1/4 cup, replaced raisins with pineapple; used hemp seeds instead of flax seeds (6T); replaced half of the carrots with shredded zucchini; switched orange juice with pineapple juice. Last of all, I replaced the apple sauce with non fat plain greek yogurt. I wanted to lower the fat and raise the protein a bit. Oh and I sprinkled a wee bit of coconut flakes on top of each muffin. Just for fun. Thanks for the recipe.

  2. Made them. Pretty darn easy. Taste really good!! I mixed in some dried tart cherries with the raisins… turned out great!! Thanks so much for the recipe!

  3. I love these delicious muffins! I made them just as the recipe states and they are moist and full of flavor. I get my “muffin fix” with healthier ingredients. I’m look forward to trying different flavors, like the addition of coconut. I see a lot of these in my future.

  4. These muffins are just gorgeous. What a great recipe. Love recipes with so much flexibility.

    As Always, thank you!

  5. Amazing muffins! They turned out perfectly! The only problem is that they disappeared too quickly!

  6. Flavor and texture is great but they are a bit too sweet for me, especially if I want to eat 2 for breakfast. I made 15 muffins and each one came out around 225 calories with 17.9 g sugar per muffin. Will definitely cut down on the sweetness next time. Thanks for the recipe!

  7. Do you think full fat Greek yogurt in place of the applesauce would work???

    1. Hi Tara, The substitutions I have testes for applesauce are melted butter or more oil, apple butter, mashed banana, canned crushed pineapple, or pumpkin puree. I haven’t tested yogurt but I do think it will work 🙂

  8. I added crushed pineapple and coconut! Mmmmm good

  9. So, I tried this recipe this morning and I LOVED it! Couple-a-few things…
    1) Usually when you bake with fresh fruit, you wring the excess moisture out of the fruit before baking with it. I did this and think I probably didn’t have to. When I combined all the ingredients together in the end, it looked a little thick. I added a little more oil and orange juice to it and it baked fine.
    2) Watch it carefully. It cooked quick (probably because my mixture was a little dryer than maybe intended and I poured slightly smaller muffins). Total bake time was 18 mins.
    3) I used the flax and love the flavor, fiber, and healthy oils it adds. I also didn’t have pecan so I used raisins and dried unsweetened cranberries. I figured with the orange and cinnamon base flavors, how could I go wrong? And, I wasn’t disappointed. I think crushed pineapple would work nicely in this to give more moisture/flavor too.
    4) Lots of fiber in these babies. Be careful when you decide to hork’em down. Have some water with it. Haha.

    Thanks for sharing a semi-healthy baking recipe. Great way to sneak in veggies and fiber for the little ones also.

  10. Hi Sally!

    My mother and I were wondering if you could use bran instead of flour. She has made morning glory muffins where she has soaked bran in milk for 30 minutes or so and it creates a nice base consistency. Just wondering if you have ever tried it?!

    1. Hi Becky! This recipe is a bit different from traditional bran muffins. I wouldn’t switch the flour with bran here.

  11. This was delicious! Based on what I had available, I used 1 cup white whole wheat flour, 1/2 cup oat flour, and 1/2 cup almond flour. I also used the coconut oil and pineapple juice options.

  12. Hello! Would it be possible to substitute maple syrup for the brow sugar? Thanks!

    1. Hi Kelsey! Best to keep it a dry sweetener. I love using coconut sugar if you’re looking for an unrefined sugar substitute.

  13. Hi Sally!
    Another delicious recipe! To make these I used both whole wheat and whole rye flour as didn’t have enough wheat flour at the time and they turned out lovely and very moist. Keeping in a fridge is a must I think. Delicious cold or heated!

  14. I’m not a baker at all, but I tried this recipe and used Quinoa flour and flax seed flour and baked in a muffin top tin with the rest of it in a bread pan. I found out I didn’t have a grater so I used a microplane, which turned out to be more mushy so I chopped the carrots as tiny as I could and added a can of crushed pineapple. Both the muffin tops and the loaf turned out great!

  15. I just made these for the first time, and even my “I don’t eat sweets for breakfast” husband is devouring them! Love the recipe! Thank you!

  16. This is currently my favorite muffin recipe!

    Such a versatile and forgiving recipe! Love love love these muffins. So far my fav combo includes zucccini instead of carrots, soaking the raisins in vanilla and lots of cinnamon (a bit more than the actual recipe suggests), subbing more oil for the apple sauce and Using pineapple juice. I also more than doubled the spices to get a spice cake like flavor. My family doesn’t eat a lot of sugar so we halfed the brown sugar to 1/4. That’s probably why we need more spices and oil to support the strong flavors we like.
    All in all, so so good. Thank you Sally!

  17. I accidentally forgot to put in eggs (my daughter was interrupting me) but they still turned out great! I will make it again with eggs and see if there is a big texture difference. Stay tuned!

  18. Avneet Bajwa says:

    Sally delivers as usual. Even my husband who has an aversion to whole wheat flour loved these! They are very tasty somewhat like a lighter carrot cake. I followed the recipe almost exactly except I used walnuts and olive oil. I look forward to eating these! And I am pretty full after as well.

  19. I made these…but I made a lot of changes….
    I used garan masala instead of cinnamon – added a nice flavor. I thought I had applesauce, but I didn’t – so I used pumpkin instead and I doubled it because I don’t have an apple… I left out the carrot… but I added dried raspberries and blueberries. I did have flax and whole wheat flour – It looked a little dry so I added a little extra milk (no orange juice). After all that – they are delicious! So great base recipe – very flexible.

    1. These are very good and satisfying. I made your favorite carrot cake for Easter and I haven’t been able to stop eating it. So, I needed a healthier alternative. After baking and eating one of these muffins for breakfast I feel like I’ve done something healthy for myself. Thanks, sally.

  20. Haven’t made these for a while and was CRAVING them….. had all the ingredients, thankfully! I used apple butter instead of applesauce because that is what i had on hand. Added the flax meal, chia seeds and used coconut oil. Ummm Ummm good

  21. one of the bestbakes. Thank u for ur beautiful n never fail recipes time n ever again

  22. Elaine Armstrong says:

    My raisins were old and dried out so I added them to the liquid ingredients and soaked for about 10 minutes to plump them up. Used some mashed banana instead of applesauce. Probably over baked them by a couple of minutes but they were still moist and not dried out at all. I will add these to my muffin rotation.

  23. Awesome recipe! These muffins are full of good for you ingredients, but are still moist and delicious and totally hit the spot when you are craving something a little sweet. Followed the recipe exactly and they were perfect.

  24. love this recipe!!! I made the mistake of halving the recipe and had to make another batch the very next day!! I’ve used both apple juice and mango juice, I’ve found that the type of fruit juice doesn’t really make a difference, so you can basically just use whatever you have

  25. I love these muffins!

    It’s great that they have so much fun stuff in them (and that I can pretty much mix and match as I please with what I have in the house). I usually use whole wheat spelt flour (they like spelt in Germany), which makes them a little more dense. I also usually reduce the sugar- sometimes I leave it out entirely and only use the honey as listed in the recipe. Needless to say the recipe is very forgiving, they taste great and have so much good for you stuff in them!

  26. I used all purpose flour but otherwise followed the recipe exactly – I would recommend way more mix-ins that listed!! WAY more raisins/cranberries, nuts, etc. Maybe that’s just my taste. Otherwise, great bake.

  27. Made these this morning. I used pistachios. Oh my! They are so delicious!

  28. This is going to be my go to Morning Glory Muffin recipe! The muffins were so flavorful and moist. I’ve tried several, several recipes and this is the best to date! Love the addition of flax meal. I also like that they are a bit more balanced and on the healthier side.

  29. Absolutely wonderful.
    I used some of your suggested changes but this recipe is a winner including baking temps and times.
    It made 14 for me.
    Thank you.

  30. These were amazing! I made them with all purpose flour and walnuts instead of pecans, and omitted the flax, orange zest and raisins because I didn’t have any. I ended up with 14 muffins. Thank you 🙂

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