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
This recipe was great! After a day, I took one out of the fridge and some of the carrots turned green on the inside! When I I thawed frozen ones and the same thing happened. Is this normal? Are they safe to eat? How can this be avoided?
Hi Cara, 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.
Just made these this morning. Used one cup of All purpose flour instead of all whole wheat.
Wonderful recipe again!
Thanks
Would it be possible to use all-purpose flour instead of whole-wheat?
Yes, absolutely. Same amount.
My family had requested this recipe more times than I can count. I use pineapple juice and it’s incredibly moist and delicious. Reminds me of carrot cake, in the best possible way!
Can I substitute apple sauce for the eggs or coconut oil?
Hi Joe, we haven’t tested an egg-free version of these muffins, so we’re unsure how applesauce would work as a swap. You can use melted butter in place of the oil. We don’t recommend leaving the fat out completely.
I have tried a few swaps for eggs…flax egg, pumpkin puree( 1/4C replaces 1 egg)
The problem with swapping is you do get less rise in your muffins or quick breads. But maybe ??? Try searching for aamount of baking soda to add.I have not tried that. Just a wild ( hopeful) wish
HI Sally and Team:
Since this makes more than 12 muffins, to save time can it be cooked in a 9 x 5 loaf pan, would it come out the same quality? If so, how long do you think it would require and at what temperature?
Hi Jenn, 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.
This is such a good recipe! My husband particularly enjoyed it. It looks and tastes both wholesome and delicious! The orange zest is This one is going into the monthly muffin rotation.
I love this recipe and make it frequently. I always wonder though why when I am making these yield 14+. Any suggestions on tweaking to make it 18?
Hi Teresa, so glad you enjoy the muffins! The recipe as written yields 14-16 muffins. You can try scaling it up a bit, or we recommend making two separate batches for best results. You can always freeze any leftovers!
If I’m making these in the mini muffin pan, do I still fill them to the top?
Hi Karen, yes, to the top! Bake 13-14 total minutes at 350°F (177°C) the whole time.
This is a keeper. It always turns out great and is a crowd pleaser. I added chopped pineapples and use the juice instead of orange juice and I also altered with using chopped dates for a reduced sugar version.
They weren’t good. I did not have OJ or any juice so added more applesauce. They were very dense. I would skip the honey next time as they were too sweet. I did not use flax seed.
Hi Ann, Thank you for trying this recipe. Substituting the juice for a thicker ingredient like applesauce would make the muffins more dense. If you wish to try it again and don’t have any juice, you can use milk instead.
I am looking at your Morning Glory Muffin Recipe. Is it necessary to grease the muffin liners? How do you recommend doing that?
Hi Dawn, I find these muffins can stick to liners. You can use nonstick spray to grease the liners or you can just grease the muffin pan without using liners.
These muffins are delicious and moist! Love that I could sneak some veggies in because my kids ate these so quickly!
I made this with oatmeal. Left the flaxseed out. They came out very moist. Delicious recipe!
If I use oatmeal flour is the same amount of whole wheat flour ? Thanks
Hi Peggy, We don’t recommend it. Oat flour won’t hold up to the moisture in the batter.
I made this recipe about 3 times. I bought a scale and started weighing my ingredients.
Turned out much better. I use the tulip muffin liner and make 12 muffins.
OMG! These are the best healthy morning glory muffins ever. Super moist. No
extra baking time needed.
Hi there! I have a question about substitutions. If I replace the grated apple with crushed pineapple, do I first drain the pineapple?
Hi Donna, yes, you’ll want to drain the pineapple first. Hope you enjoy it!
This recipe looks great! If I make the batter ahead and keep in the fridge overnight + bake the following day, will the texture be compromised?
Hi Erin! You rise the batter not rising properly rising if made ahead of time. We don’t recommend it.
Amazing!!! I used GF flour (a 1:1 brand), added an extra egg and used milk for extra protein. I cooked this at a high altitude so it took a little longer to bake. Unbelievably delicious and moist!
Another fabulous recipe! Moist and delicious.
This was the best morning glory muffin recipe I’ve tried!
this was one of the best muffin recipes I have ever done. So delicious. I loved the orange flavor – and apple, and all other great flavors. It was a bit of preparation, but so worth it. Thank you.
what to use in place of flax seed
Hi Don, the flaxseed is optional, so you can simply leave it out.
What are the calorie and nutrient contents per muffin using small paper liners?
Hi Phil, We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076
Instead of using brown sugar, can you just use honey in this recipe (use 3/4 cup
Of honey)
Hi Erika, we don’t recommend using ALL honey for this recipe. Coconut sugar is a dry unrefined sugar you can use in the place of brown sugar.
Muffins turned out perfectly moist. I left out the nuts and apple sauce. I added coconut and crushed pineapple. Will be making again. Thanks for all the substitutions. So helpful.
This recipe is perfect. It made 16 muffins. I added allspice and crushed pineapple.
I’m gonna give you five even though, maybe it’s only 4.76, I don’t want to be stingy the recipe as a large whole is very good, and it was very forgiving with substitutions. I read diligently about others, suggesting these wanted less time in the oven, but my toothpick came out, moist every time, but that’s only because of the ingredients! I suggest at least two minutes less than the 18 recommended
They’re a little bit more work than a standard muffin with the shredding but soooo worth it! I made them just as written except used lower glycemic coconut sugar instead of brown sugar. My husband loves them! Thanks Sally!
OOps! forgot include nutrition info from https://www.verywellfit.com/recipe-nutrition-analyzer-4157076: servings: 12, calories/ serving: 257, total fat 8.3g: 11% , total saturated fat 1.6g: 8%, cholesterol 93mg: 31%, sodium 6229mg: 271%, total carbohydrates 36.7g: 13%, dietary fiber 5.4g: 19%, total sugars 13.1g: protein: 6.9g; vitamin D 9mcg: 44%, calcium 92mg: 7%, iron 3mg: 14%, potassium 296mg: 6%