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 here, so you can truly make them your own.
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!
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 wholesome ingredients like fresh fruit and vegetables, applesauce, flaxseed, 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. 🙂
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 flaxseed are totally optional, but I usually add both for extra flavor.
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. (Or use a mix of both, like I do for peanut butter banana muffins.) 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 (dairy or nondairy) 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!
More Healthful Baked Goods
- Whole Wheat Banana Bread
- Breakfast Cookies
- Chocolate Zucchini Bread
- Baked Apple Cinnamon Oatmeal Cups
- Chocolate Banana Muffins and Blueberry Banana Muffins
- Bran Muffins
- Vanilla Almond Granola or Pumpkin Granola
- Chocolate Chip Baked Oatmeal Cups
And for even more inspiration, see my complete list of 30+ healthy breakfast recipes.
PrintMorning Glory Muffins
- Prep Time: 30 minutes
- Cook Time: 24 minutes
- Total Time: 1 hour
- Yield: 14-16 muffins
- Category: Muffins
- Method: Baking
- Cuisine: American
Description
Filled with healthy ingredients like whole wheat flour, flaxseed, 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.
Ingredients
- 2 cups (260g) whole wheat flour (spooned & leveled)
- 2 teaspoons baking soda
- 2 teaspoons ground cinnamon
- 1/2 teaspoon ground ginger
- 1/2 teaspoon salt
- 1/3 cup (35g) ground flaxseed (optional)
- 3 large eggs, at room temperature
- 1/2 cup (100g) packed light or dark brown sugar
- 1/4 cup (85g) honey
- 1/3 cup (80ml) vegetable oil, 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
Instructions
- 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.
- Whisk the flour, baking soda, cinnamon, ginger, salt, and flaxseed 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 until just combined and no pockets of flour remain.
- Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425°F; 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. Allow the muffins to cool for 10 minutes in the pan, then transfer to a wire rack to cool until ready to eat.
- Cover leftover muffins and store at room temperature for 2 days or in the refrigerator for up to 1 week.
Notes
- 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.
- Special Tools (affiliate links): 12-count Muffin Pan | Muffin Liners | Box Grater | Glass Mixing Bowls | Whisk | Wooden Spoon or Silicone Spatula | Cooling Rack
- Substitutions: See blog post above for all substitutions I’ve tested.
- 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 (except mini muffins; see next Note).
- Mini Muffins: If making these in a mini muffin pan, bake 13–14 minutes total at 350°F (177°C) the whole time.
- 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
Here is the nutrition information from https://www.verywellfit.com/recipe-nutrition-analyzer-4157076 without ground flaxseed, with orange juice and with walnuts instead of pecans. All other ingredients are as called out in recipe
This is a fantastic recipe! I made the following substitutions: chia seeds instead of flax meal, pear butter instead of apple sauce. My family LOVED them!
★★★★★
I made this with all buckwheat flour and they were so tasty! I also swapped mashed bananas in place of apple sauce and almond milk in place of OJ just bc I didn’t have either ingredients. My kids (2 & 4) LOVED them. I did too!
I enjoyed these muffins, I would also add some fresh blueberries on the tops and it was Divine!!
★★★★★
I enjoyed these muffins, I would also add some fresh blueberries on the tips and it was Divine!!
★★★★★
I love your muffin recipes! If I want to turn these recipes into JUMBO muffins, what would I do for temperature and time changes?
Hi Kylie, for jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
Made some for my college students for morning class….without the nuts…well received by everyone!
Thanks
★★★★★
Such a great recipe! I see maple syrup instead of the honey, dried cranberries (I had no raisins) and sweetened coconut flakes (we have a nut allergy in the family) and I have 16 beautiful muffins ready to be eaten. I am going to package a few up as a hostess gift for my friends. They are cooking us dinner, I have part of their breakfast covered.
Can this recipe be baked into a bread?
Hi Linda, absolutely! We’re unsure of the exact bake time, but you can use the baking time and directions from this harvest spice bread as a guide.
I had some carrots and apples that needed to be used and remembered that there was such a thing as morning glory muffins. I used ap flour, no flaxseed, low sugar maple syrup instead of honey, olive oil, low sugar craisins instead of raisins. Accidentally I left out the brown sugar. I also added about 1/4 cup of unsweetened shredded coconut. The muffins turned out beautiful. I made 12 regular muffins and 7 mini muffins. They definitely need that brown sugar that I mistakenly left out but they are still good.
★★★★★
These are wonderful! Made a batch yesterday and eating one for breakfast this morning!!
I thought these were just ok. What I liked most about them was the idea that they were somewhat healthy. However, I cannot say that they had much taste, and believe me, I am not one who likes things very sweet, so the sugar factor was not the problem. I recommend them for people who are looking for a bit more of a healthy muffin, though.
★★★
I made these this morning and followed the recipe. The muffin I tried tasted salty. The recipe calls for 2 tsp of baking soda and 1/2 tsp salt, which I did. Any idea why the salty taste?
Hi Barbara, we haven’t had that feedback before, very interesting! Did you happen to use salted nuts in the muffins?
I only had that happen 1X. ( out of many times making these). I now add a note in my recipe print out to whisk dry ingredients REALLY well. The problem has never happened again. So I am guessing my salt did not get mixed in well enough. Also be sure you are not using sea salt. That gave a salty taste to my friends batch. Once she switched she said no more problem.
★★★★★
I’m so excited to make these! I LOVE morning glory muffins. They’re my absolute favourite. Question — can you recommend cooking time if I were to do the big sized muffins (the ones that are 6 per pan?)
Hi Christine, for jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
Can you aCan you add a disclaimer to the baking step of this recipe? I mave made this recipe several times and every single time i miss the step about reducing the heat. Maybe something in bold or highlighted in the step recommending the reader to read carefully.
Thank you for the feedback, we will look into re-wording this!
I’m made this twice – they were delicious both times!! I have a fairly new Wolf oven and found that the muffins only needed to bake for 10 minutes after turning the temp down to 350 degrees.
★★★★★
Oh My these are wonderful! My husband and I made these last night with what we had on hand. Made a double recipe with 3/4 wheat and 1/4 AP flours. Used hemp hearts instead of flax seed, 4 cups of mixed shredded carrot and zucchini, 2 cup apple (one granny and one honeyscrisp). Used melted coconut oil for the fat, crancherries and half pecans half pipits. What a fabulous recipe! We got 24 standard and 34 mini’s. Lots frozen for breakfast/snacks and the mini’s are on the way to my work site, for I’m sure amazing reviews! Thanks Sally! and Happy New Year!
★★★★★
These Morning Glory Muffins turned out perfect! I used mashed bananas instead of the applesauce but otherwise followed the instructions exactly. Great idea to start out with a 425 degree oven for 5 minutes followed by 350 degrees for 18 minutes as the muffins had high domes and were very fluffy and delicious!
Thanks for sharing about your substitution! I wanted to make these this morning but I don’t have applesauce on hand. I have bananas though and now I’ll move forward with that a little more confident! Woohoo
I can’t stand the taste of flaxseed. It says this is optional, but if I’m not using it, shouldn’t I substitute something else since 1/3 c of something is quite a bit to just leave out.
Hi JEK, you can just leave it out!
Sometime, you can experiment w/ chia seeds. They have NO taste at all. PLUS they have much more fiber and protein than flax seeds OR you can add more nuts ( smallish chopped, about 1/4 C. )if not alergic.. But, as Sally said, you can just omit the chia seeds. They DO turn out tasting the same. Store the chia seeds in the fridge in an air TIGHT container though.
★★★★★
I’m curious why you used three eggs instead of the typical two for muffins. I’m sure there is a reason! Would you mind sharing it?
Hi Charlotte! With all the delicious and hearty add-ins in this recipe, we needed extra binding from the eggs.
Hi Can I make these with white all purpose flour
Hi Aline, Sure can!
I LOVE these! I freeze the batch and take one to work every morning. The best.
★★★★★
I made these muffins hoping it would taste like the ones Whole Foods used to make. Not exactly but close. Made regular size and mini. Good flavor and easy 1 bowl mix.
★★★★★
Hi Sally and Team: Happy New Year! Using a gluten free white flour, would adding some Molasses help make up for the missing flavor and texture of the Whole Wheat Flour?
Hi Jenn, we haven’t tested these muffins with a gluten free flour, so we’re unsure of the results. You can try adding a small amount of molasses for flavor, but be careful not to add too much as the additional liquid will change how the batter bakes up. Let us know what you try!
Deliciously moist!! Love all the optional substitutions and baking tips!
★★★★★
While a great base recipe thay ill use again, it was a little lacking in flavour for me…next time I’ll add some coconut perhaps and some allspice or something? Texture great inside but tops weren’t “crunchy ” around the edges. Deepite being fully cooked. Not sure how to fix that?
★★★★
I love this recipe!! Absolutely my favourite!!! I make these muffins weekly. Now, there have been times the 3 cups if fruit and veg may be different in measurement, but always carrot, apple and zucchini. It is a success everytime. Thanks for sharing ❤️
Hello! I saw your notes about the gluten free flours to steer clear of. Do you think it might work subbing the wheat flour with the bobs 1-1 gluten free flour?
Hi Sarah, we haven’t tested this recipe with gluten-free flours, but some readers have reported success using 1:1 flour substitutes (like Bob’s). If you try it, let us know how it goes!
Thanks for the quick response! I was able to make these this morning as the gluten free 1-1 flour worked well, thanks! They were delicious and know my toddler will love them too. I subbed the honey for maple syrup and the brown sugar for coconut sugar. Thanks again for a wonderful recipe!
★★★★★
I love these muffins but am wondering if it can be made into bread too gift for the holidays.
Hi Nicole, absolutely. You can make this in 1 9×5-inch loaf pan or several smaller loaf pans. Bake time will vary depending on the size of your pan, but keep a close eye on it and use a toothpick to test for doneness.
I made these for the first time today and my husband loved them! Is there any way to make them jumbo sized, like the Jumbo Blueberry Muffins? I make that recipe often and I’d love to convert this morning glory recipe to achieve the same oversized results!
Hi Jill, you can make this batter in jumbo muffin pans, following the bake time and directions from the jumbo blueberry muffins as a guide. Glad you enjoyed these!