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
Can this be made into a loaf if I don’t have muffin cups
Hi Celeste, 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 replace the honey with mashed banana for sweetness? Thank you!
Hi Mary, no, mashed banana will add too much additional moisture in place of the honey. You can use brown sugar, coconut sugar, or pure maple syrup instead of the honey. If you wanted to incorporate banana somewhere, you can swap it for the applesauce. Enjoy!
I used to purchase morning glory muffins from a local coffee shop that has since closed. They were a favorite breakfast treat! I have seen other recipes that include Greek yogurt to add protein. I trust your recipes more than others I see from untested providers. Can you provide any guidance on how Greek yogurt could be substituted or added to your recipe? Thank you so much!
Hi Terri, we haven’t tested it, but several readers have reported success with subbing Greek yogurt for the applesauce in these muffins. If you try it, please let us know how they turn out!
Lots of ingredients but so tasty!! I did do half wheat flour and half AP flour. Thanks Sally!
I used Arva Flour Mill’s Whole Emmer Flour and the muffins turned out beautifully. The batter seemed to be rising after stirring in the wet ingredients. The muffins were fluffy and light and not too sweet. I’ll be making these again and again.
Great recipe. Love these muffins. I added shredded zucchini with.one cup of shredded carrots. They are delicious .
Wow, are these nice! I so appreciate the gram measurements. Not only for accuracy, but clean up – no more measuring cups to wash. And all the helpful substitution ideas! Yay!
I used freshly ground soft white wheat and subbed coconut sugar and avocado oil. I soaked my raisins in boiling water, then used the drained liquid instead of the juice. Oh, and I sprinkled the tops with coarse sparking sugar for glitz.
These were done at 20 minutes. I love the high mountain tops!
Wonderful texture and flavor. And I feel like they’re actually breakfast worthy instead of an unhealthy sweet treat. Thank you. These are KEEPERS!
These were hands down THE most delicious ‘healthy’ muffins I have EVER made! They were SO delicious, that I am willing to deal with all the various ingredients, something I would normally avoid lol. I will double batch them in future, hopefully they freeze well?
We *LOVE* these muffins! I like to take them camping with us since they make for an easy and healthy light breakfast or snack.
Dear Sally, I love reading your recipes and all the effort that you and your staff put into this beautiful e-mail that you send. Your ingredients are carefully selected for the best outcome. I recently made the pumpkin spice with the black pepper. I love adding it to my coffee. It is a treat. Thank you for your commitment to excellent recipes, and I’m saving this one to make my son for valentines day.
These are amazing! And easy! I didn’t have carrot, so used all apple. I added more cinnamon than was called for as well as added nutmeg, allspice, and cloves.
Will definitely make them again! Love baking with whole wheat.
Can this be made in a loaf, as bread?
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!
I make these muffins about every couple of weeks. They freeze so well. They are delicious and very satisfying.
Can I replace the oil with butter?
Yes!
How long to bake this muffin for jumbo muffins? Is the baking method the same? How many jumbo muffins ?
Hi Deb! We’d use this morning glory muffin batter with the bake times and instructions from these jumbo blueberry muffins as a guide. Hope they’re a hit!
They need to be sweeter for me and more salt.
Hi DeeDee, thank you for giving these a try. The sweetness can vary a bit depending on the exact add-ins/ingredient swaps you make, so feel free to experiment with the ingredients if you wish to try these again. You could also increase the salt slightly.
Do you think I could make these as a loaf with the same measurements?
Hi Ana, absolutely. Bake at 350 for the entire time. Bake time will be much longer—keep a close eye on it and use a toothpick to test for doneness.
I love this recipe, it’s so nice to have options if you don’t have an ingredient! I used peanut oil in place of apple sauce, cut up dates in place of raisins, and chopped almonds instead of pecans! It all worked out.
Can these be made with gluten free flour?
Hi Barb! 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!
Holy cow! These muffins were incredibly delicious. I used half dried cranberries and half raisins, as well as substituting almond flour for half of the flour and oat bran and wheat bran in place of some of the flour as well – even with all of those tweaks these muffins were so good! I will definitely be making them again.
These are by far the best Morning Gloey muffins I have ever made. They are a bit tome consuming but well worth the extra effort.
If I could give them 20 stars, I would!
I have your cookbook and enjoy those recipes and I thank you so much for all of that. I would love to be able to take advantage of your website recipes but the site has so many ads that I can only see a couple of inches of your content. Very frustrating……
Hi Sherrie, thank you for the kind comment and for using my cookbook! We’re aware that an intrusive Amazon pop-up ad has unfortunately reappeared, and we’re so sorry about the frustration this causes. Despite multiple safeguards in place, it sometimes slips through under different labels, which makes it harder to catch until it appears live on the site. We flagged it with our ad network first thing this morning and have requested another block, so hopefully it’s resolved again shortly. We truly appreciate your patience; this has been frustrating for us as well, and we’re continuing to stay on top of it!
Can I use sweetened applesauce?
Hi Sheena, you can use sweetened applesauce with no other changes. Enjoy!