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!
PS: Try them with a swipe of homemade honey butter. What a treat!
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.
Print
Morning 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 (80g) 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.
Reader Comments and Reviews
These are delicious. I have been on a sourdough journey and I substituted 50 grams of the orange juice and 50 grams of the wheat flour with 100 grams of active sourdough starter and it worked out perfectly. Thanks for always including weight measurements in your recipes! It made this addition very easy!
These are delicious. I have been on a sourdough journey and I substituted 50 grams of the orange juice and 50 grams of the wheat flour with 100 grams of active sourdough starter and it worked out perfectly. Thanks for always including weight measurements in your recipes! It made this addition very easy!
cant wait to try these muffins! Do u know what the internal temperature should be when baked? Thank you.
Hi Joan, usually about 200 degrees F, but we just use a toothpick to test for doneness with muffins – it works great!
Can I use bran flour in place of the wheat flour?
Hi Kira, we haven’t tested this recipe with bran flour so we’re unsure of the results.
Question can I do chopped apples instead of shredded/grated I don’t have a standing grater and buying one would be expensive if I chop them super finely would it still work?
Hi Anna, yes, you can chop them finely, that should work here. Enjoy!
I absolutely love these muffins as does the whole family! My question is can you double the recipe or is it better to make 2 batches?
For best results, we recommend making two separate batches rather than doubling.
How would I make & bake these as a GF option? I LOVE the GF BB and Peach crisps and time to try something new……
Hi kt, We haven’t tested this recipe with gluten free flours, but some readers have reported success using 1:1 flour substitutes (like Cup4Cup). If you try it, let us know how it goes!
This is a wonderful and adaptable recipe. I have made it 3 times (the first as writen).
I initially tried it as 1/2 the original as I did not know how it would turn out.
I have used almond flour and regular flour, 1/2 whole wheat and white flour and 100% whole wheat. Have substituted avocado for the apple sauce, omitted the brown sugar (already sweet enough with orange juice). All gave turned out great. Have also substituted chia seeds for the flax (error on my part but equally tasty).
The final thing I tried was making this as a 8 x 8. Baked at at 425 degrees x 5 minutes and then 350 degrees for 45 minutes. Excellent!!
These muffins are moist and delicious. I chose to use coconut oil. The only recipe change I made was using a pear instead of an apple. I would highly recommend this recipe.
These are good! Mix was a little thin after adding grated apple, carrot, and zucchini (directions did not say to squeeze out liquid), and I had a medium orange for the zest and juiced the whole thing, did not measure, applesauce too. So I added more flour and then 2 small crushed bananas and it was great! This made 23 muffins for me. They were good!
How do I make these into the jumbo muffins?
Hi Carol, for jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
THANKYOU
I made these for my toddler and he loves them! Subbed an overripe banana for brown sugar and it worked amazingly! I love them too!
Could this be baked in a loaf pan like a quick bread? Or in a small bundt pan like a cake?
Hi Janet, absolutely, you can bake this in a 9×5-inch 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. You can bake at 350 degrees for the entire time. Enjoy!
Hello there! I was looking for a healthy recipe for muffins for my kids in the morning on schooldays. I must say, I was a little skeptical. But boy was I wrong. I stayed up late tonight, made a batch. They rose beautifully and was super easy to take out of my muffin tin. Substitutions I made: I didn’t have applesauce on hand so I mashed 1/3 cup banana. I didn’t have light brown sugar so I measured 1/2 cup white sugar and mixed in 1/2 tablespoon molasses. I didn’t have oils called ( ran out tonight) for so I used unsalted butter. I skipped the raisins and nuts because my kids don’t like them in their muffins. This recipe is such a winner! I will be passing it down to my friends and family. Thank you!! I will keep you all posted to see what my kids think.
I was worried about all the ingredients in this recipe, but thought that I would try it regardless. Imade this recipe as written with the exception of substituting the whole wheat flour with regular flour and coconut flour. I made a half recipe because I wasn’t sure about all the carrot in the muffin. So I use three-quarter cups white flour and a quarter cup coconut flour. I was a bit worried about using the flaxseeds as they absorb moisture. The batter was dense when I placed it in the muffin tins. When baked, they turned out incredibly moist and delicious! Thank you for this wonderful recipe.
We really enjoyed these muffins! Definitely the most moist, all whole wheat flour, muffin I’ve ever made. I added dried tart cherries, raisins and slivered almonds and there was wonderful flavor in each bite. Thank you for a terrific recipe!
I’d love to put in about 1/2 to a whole cup of pineapple tidbits, — do you think they’d work as an add-in or a substitute for any other ingredient, or would they bog the muffin down? Also, can you substitute yogurt for the applesauce (don’t have any toddlers, so I don’t typically have any on hand!)? Thank you so much for your wonderful recipes and advice, Sally!
Reena
Hi Reena, yogurt *should* work for replacing the applesauce, or see post above for several other substitutions. Pineapple tidbits should act more as an add-in, although they have more moisture than add-ins like raisins or walnuts. We’d start small, say 1/2 cup of pineapple tidbits, in place of some of the raisins and nuts, keeping the total amount of add-ins to about 1 cup. If the moisture level seems okay, then you can try increasing the pineapple for the next batch. Hope this helps and let us know how they turn out for you!
This recipe is one of my staple Sally recipes that I make again and again and it never fails to impress. My personal recommendation for peak deliciousness is to reheat the muffins in an air fryer (350 degrees F for 5 – 6 minutes is the sweet spot for me). This gets the outside beautifully cripsy while the inside is super warm and delicious.
Can you substitute brown sugar for coconut sugar?
Hi Mala, yes, same amount.
I have tried several Morning Glory Muffin recipies and this one is, by far, my absolute favourite!! I substituted crushed pineapple for the applesauce and they were absolutely scrumptious!! Thank you for sharing this amazing recipe with us to enjoy!
These are great! I was able to make them with only two eggs because that’s what I had on hand and they turned out great! I did add the flax meal so that probably helped.
these are the best muffins I’ve ever eaten! They weren’t very tasty the day that i made them but the next day they were so good. I gave some to 2 of my friends who don’t like anything made with whole wheat flour and don’t like muffins… they both asked for the recipe and said they were fabulous!!!!
Excellent flavour and texture. I didnt have an apple so I used fresh pineapple. Also, no honey in the house so I used maple syrup. Finally, since I was bringing them to a GF friend, I used President’s Choice All-Purpose flour 1:1 with no problems. Thanks for a great recipe (as usual).
Unfortunately, I didn’t have all the ingredients I needed so I made some substitutions: I used regular flour instead of wholewheat, I replaced the applesauce with fresh pineapple that I blended up with some water until it was the same thickness as applesauce, I used apple juice instead of orange juice, I replaced some of the carrots with more apple and some finely chopped pineapple and I replaced the nuts with sunflower seeds. I also left out the raisins and chia seeds, added some poppy seeds and reduced the sugar to 1/3 C because of the pineapple and apple juice. Despite all the changes, they still came out really good. It’s nice having a healthier recipe that I can adapt to use what I already have on hand.
I have not made these yet it they sound amazing and based on a recipe nutrition calculator I ran, they have 268 calories each based on 14 muffins and 11.5 grams of fiber!
So good!
I’ve made these three times already, looked these up when I had a single orange to use up and apple sauce. Glad I did, these are excellent.
First time I didn’t have flax or raisins, used half bread and half all purpose flour and I loved them!
Second time I added flax, dried cranberries and half whole wheat half all purpose – note do not use crystallized honey it was much much drier.
Third times the charm! I added a little more apple sauce, more orange juice, more shredded apple, liquid honey and it was perfect.
Will definitely make again, but might leave out the craisins, overall it makes it a bit too sweet for me (even when with half the amount)
Hi Sally and team!
I’m about to try this recipe, but was unable to find unsweetened applesauce. If I use sweetened, should I reduce the sugar or honey amounts? Note that I’m also planning to use crushed pineapple in place of shredded apples.
Many thanks as always-
Jo
Hi Jo, you can use sweetened applesauce with no other changes. Enjoy!
Thanks Lexi – the muffins turned out great! Sally’s guidance in the post and comments from readers are spot on – the muffins are moist and flavorful and can really be tailored to suit individual preferences/tastes. Thanks again for another great recipe!
Can you bake this recipe in a loaf pan instead of muffin tins?
Hi Johnna, absolutely, you can bake this in a 9×5-inch 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. You can bake at 350 degrees for the entire time. Enjoy!
Can I use 2 eggs rather than 3 as the price of eggs is thru the roof right now?
Hi Jan, we understand the want for less eggs! Three eggs really is best here, perhaps you could try replacing one of them with a “flax egg” egg substitute – we would do a quick google search for details.
I frequently use the flax in place of an egg as I have one Vegan in my family. Honestly, not noticeable- even to those of us who do eat eggs. Here is the substitution I have successfully used: 1 tablespoon ground flaxseeds,( also known as flaxseed meal) and
3 tablespoons water, mix well with a fork and let stand 10-15 minutes until congealed— equals 1 whole egg.