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 weโre 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 requiredโjust use a whiskโand 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 hereโthe morning glory muffins will taste rubbery.)
Think of these as my reader-loved harvest spice bread, but in muffin form. ๐
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 flourย (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 425ยฐF (218ยฐC). Spray a 12-count muffin pan with nonstick spray or use greased/sprayed cupcake liners. This recipe yields 14โ16 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 425ยฐF; then, keeping the muffins in the oven, reduce the oven temperature to 350ยฐF (177ยฐC). 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 23โ24 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 13โ14 minutes total at 350ยฐF (177ยฐC) 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
Hello Sally, can you replace flaxseeds with chia seeds?
Thanks so much!
Should be fine, Jane!
If I use sweet applesauce how should I adjust the sugar?
Hi Linda, you can use sweetened applesauce with no other changes. Enjoy!
Could bran flour be substituted partially for some of the wheat flour?
Hi Hannah, we havenโt tested this recipe with bran flour so weโre unsure of the results.
Made these last night. Theyโre pretty good but next time I will skip the honey because I found them a bit too sweet for me personally. No coconut? I thought that was standard in MG muffins. Anyway, I will make again with less sugar but I might add some coconut! Oh, I didnโt have raisins but did have dried cranberries and they worked wonderfully. Thanks Sally!
Made these last night. Theyโre pretty good but next time I will skip the honey because I found them a bit too sweet for me personally. No coconut? I thought that was standard in MG muffins. Anyway, I will make again with less sugar but I might add some coconut! Oh, I didnโt have raisins but did have dried cranberries and they worked wonderfully. Thanks Sally!
How long to bake for jumbo muffins?
Hi Lori, for jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
Sally can I make this as a loaf instead? Thanks!
Hi Shannon, absolutely, you can bake this in a 9ร5-inch loaf pan without making any changes to the recipe. Weโre 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!
These came out excellent! I followed the recipe exactly, with the exception of swapping some dried cherries instead of raisins (I don’t like raisins!). My kids and I are officially obsessed with these and we can’t wait to make them again. I wonder if I could use pre-shredded carrots next time though? My only complaint is that this recipe takes a long time to prep the ingredients with all the peeling and grating. Worth it, but I am always looking for a good shortcut.
Hi Ashley, pre-shredded carrots are much too dry. We recommend freshly grating your carrots for best results. Do you own a food processor? Many come with a shredding attachment that would make quick work of that part. Glad you enjoyed these!
Hello, Sally! Is it okay to substitute the brown sugar and the honey for equal amount of coconut sugar? Or, would the recipe do good with maple syrup instead of honey? Thank you so much. This recipe looks delicious!
Hi Sam, you want a liquid sweetener if substituting the honey, so we would use maple syrup!
Thanks so much!!
Hi Sally, if I am making adding zucchini, carrot and canned pineapple, what quantities should I be using for the morning glory muffins?
Hi Kay! You can replace the shredded apple with zucchini (1 cup shredded zucchini). You can replace the applesauce with canned crushed pineapple (1/3 cup pineapple). Leave the carrot quantity the same (2 cups).
Great recipe!! Thank you!
Second time making these amazing muffins. Hereโs what I changed this time. Substituted 1/2 cup whole wheat flour for Keto flour. Added two more carrots and one small zucchini. No raisins, added some walnuts. Used the not 1/2 apple. Added another couple tablespoons honey and tablespoon black strap molasses. They were even better this time.
I plan to leave out the 1/3 cup ground flaxseed. Should I add more flour to compensate for that??
Hi Jane, the flaxseed is optional, so you can simply leave it out.
Thankyou I love reading about all so yummie.
I made these because I had a lot of leftover ingredients I wanted to use up. So I used a bunch of the suggested subs – mashed banana, shredded apple, pineapple and pineapple juice. I skipped the orange zest (didnโt have it). And anyway they came out so great! I ended up with 12 regular muffins and like 15 mini. Thanks so much for all of the suggestions! Super helpful!
I just finished making them and theyโre so dense. Iโm not sure what I did wrong. I followed the recipe exactly did not over mix and it was so sick.A the only thing that I did not add was black seeds and honey. Can you give me some advice?
Hi Chantelle, these are a heartier, denser style muffin, but leaving out the honey is leaving out some crucial moisture. If you don’t have honey, you can use brown sugar, coconut sugar, or pure maple syrup instead.
I made these the night before a neighborhood 5K run so that we’d have something quick and nutritious in the morning. These were great! A family member has an egg allergy, so we used Bob’s Red Mill Egg Substitute and it worked great – excellent, moist texture, did not miss the real eggs one bit. I added a handful of shredded sweetened coconut for a more tropical flair. I baked in mini muffin tins for exactly 13 minutes as suggested. They tasted better the day after making them. This is a winner!
Perfect! Thanks for giving these a try, Barbara.
Iโve never been fond of Morning Glory muffins. This recipe changed my mind! Moist, delicious and healthy, itโs a winner in my opinion!
I’ve made them as posted so many times and they are incredible! Has anyone ever tried olive oil?
I found these muffins to be very bland out of the over. However, after sitting for 24-48 hours the flavour improved. I love the texture.
Even my husband enjoys these muffins, very unusual since he refuses to eat carrot cake. They are wonderfully moist and satisfying.
BTW, there is a very annoying Amazon ad that comes up when i open the site at this recipe. It covers the instructions. Other ads that follow are fine.
So yummy! I had 2 with my morning coffee, will definitely make these again
Love these! Super moist and I love the mixture of the different textures.
Best muffin I have ever had.
My favorite cake is carrot and this is a nice unsweet version.
I have to resist eating them all.
Delicious, healthy, and completely foolproof! After making them twice, I started doubling the recipe to make enough for my whole family to breakfast/snack all week. I like to double the apple and add dried cranberries and crumbled pecans. The result is moist, filling, and so so satisfying. Everyone in my family usually hates nuts, but this recipe has changed their minds! Pecans are a good source of healthy fat, and flaxseed’s high fiber content helps with digestive motility. My mom loves carrot cake, my dad loves orange-cranberry bread, and my grandma has a low-key problem with taking too many laxative pills… This is the perfect recipe for my whole family’s needs! Thanks as always for sharing your magic touch!
Really love! Have made several times.
Hi I was wondering if I could add chia seeds and if so how would you do it .
Hi Shauna! We would try replacing the ground flax with chia seeds.
I’d like to try freezing the morning glory muffins. What’s the best method?
Hi Faye, These muffins freeze well for up to 3 months.
I wrap them individually in plastic wrap so I can easily grab just 1 from the freezer.
I loved the recipe for Morning Glory Muffins. Healthy, moist and delicious. The texture and spices were perfect.
Any way to make this in bread or cake pan?
Hi Melany, Absolutely, you can bake this in a 9ร5-inch loaf pan without making any changes to the recipe. Weโre 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!
These muffins are delicious. I followed the recipe and they came out moist and yummy. Thank you so much.
Hello, has anyone made this without the honey? I want to give to my baby and toddler but donโt know how to sub out the honey. Thank you!
Hi Olivia, you can use maple syrup instead. Enjoy!
I made it without honey for my toddler, and added in a very ripe banana . I’ve also experimented with shredding different vegetable vegetables, such as zucchini in it and blending the eggs with spinach and adding to it. This recipe seems to be very forgiving and is a great option for toddlers since it’s low sugar.
I made it without honey for my toddler, and added in a very ripe banana. I’ve also experimented with shredding different vegetable vegetables, such as zucchini in it and blending the eggs with spinach and adding to it. This recipe seems to be very forgiving and is a great option for toddlers since it’s low sugar.