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
My favorite muffin, and I’ve never made them at home before. These are perfect! First try and they came out so tasty with the perfect texture. Can’t wait to try another round for guests!
One more comment… I didn’t have any juice so I used apple cider vinegar instead. What a forgiving recipe, still came out great.
Can you use fresh squeezed orange juice for these muffins or does it need to be store bought orange juice? I have a ton of oranges on my tree and would love to use them up. Thank you!
Hi Becky, fresh would be lovely!
This was a really good recipe and easy to make. Used all the ingredients but skipped the orange peel and used all purpose flour.
Don’t have any applesauce. Could I substitute more vegetable oil?
Hi Betty! See blog post above for substitution ideas: If needed, replace with melted butter or more oil, apple butter, mashed banana, canned crushed pineapple, or pumpkin puree.
Delicious!! My new addiction. First time I made them I did the pineapple & honey. Second time I did apple & maple syrup. Both were great, but the apple & maple syrup combo is my favorite. I can’t stop eating them. Thanks for the recipe
So delicious! I followed the recipe exactly except for omitting orange zest which I will add next time I make these muffins (likely soon given they were a hit!) I also put a little extra effort into whisking my egg and sugar together to stiffen up the eggs before adding the other wet ingredients and the final texture ended up less dense and more airy that way!
In your morning glory muffins why bake a at 425 temperature for 5 minutes and then at a lower temperature
Hi Sandra! See recipe notes for details, this helps the muffins rise tall.
I have always loved this recipe!
I am wondering if I can make the batter the night before and follow the same recipe?
Hi Carolyn, We don’t recommend making the batter ahead of time. Once the wet and dry ingredients are mixed together, the leaveners are activated and it’s best to make the muffins right away. You could make them in the evening and simply warm them up in the morning!
When it is not suggested to make a recipe ahead of time but find the ingredients list rather long, I prepare all the dry ingredients in a bowl ahead of time and leave the wet ingredients (which most often requires less time to pull together ) when I am ready to bake. Never had an issue doing this so far.
Great work Sally !
I don’t usually leave reviews because I always have to modify recipes to accommodate my daughter’s egg allergy. But, I made this with “flax eggs” instead of real eggs, omitting the optional extra 1/3 cup of flax seeds, and I think they turned out great! I left out the nuts (again due to allergies), but I think next time I try the suggested substitution of sunflower seeds. I will definitely be making these again!
This recipe has a lot of components and a lot of prep work but it’s so worth it. I love it
I made these years ago, and they were so great!
I did have a question on whether i can substitue the wheat flour with oat flour?
I have a bunch of oats and am looking for recipes to use them
Hi B.M. Oat flour has very different baking properties than whole wheat flour, so your muffins may come out a bit crumbly. If you give them a try, please let us know how they turn out!
Way to many eggs mine came out to dense and dry tasting I would skip the honey and just add 1 cup of brown sugar and 2 eggs I also would say that cooking time was to long and didn’t want to crust up as nicely I didn’t like this recipe at all and wasted a lot of money making it.
I love morning glory muffins. I felt that my batch was not sweet enough. I used to buy a morning glory muffin from a coffee shop nearby. The texture from this recipe seemed right, but I plan to try this again with more sugar and maybe more cinnamon.
Hi, I love the muffins, but what does it mean when the batter sticks to the paper liner? What do I do to fix that next time?
Hi Jenny, are you using high-quality paper liners? Unfortunately, some simply stick more than others. Be sure to also let the muffins fully cool before taking off the liners. If they’re still warm, that can cause some of the muffin to stick. Glad you enjoyed the muffins!
This is my second time making the muffins. I blend the carrots and zucchini, and all the wet gradients together, excluding the eggs. This is the hide the vegetables for my toddlers. I cut also the sugar in half and only use a quarter cup and use the pineapple substitute and exclude the walnut. We love this recipe. Thanks.
Can you make this into a loaf?
Hi Amy, absolutely! You can bake this in a 9×5 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.
Hi! I have a question. What would you recommend if I wanted to make these muffins gluten free? Excited to try the recipe 🙂 Thank you
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!
Disappointed the second time I made these…..
Maybe I should try adding the orange zest if I make these a third time. I was expecting a muffin with more flavor. I felt these were just blah tasting, like there were too many ingredients vying for the breakout flavor. Too much shredding of ingredients, carrots and apple, in my case, to end up not tasting like anything. Sorry to everyone else who loved the recipe.
I made these omitting flax seed (because I did not have any) and using maple syrup in place of honey. They are yummy and moist. It made 13 standard sized muffins. Don’t skip the orange zest, it adds a great orange flavor to the muffin. I put most in the freezer to enjoy later. Thanks for the great recipe.
Thank you Sally for info on baking soda STARTING to expire or go bad. I did not know that it changed the taste…..dah. I too was concerned about the amt of baking soda….BUT mine had NO metalic taste. You do include enough acidic ingredients to fully utilize the baking soda. Erica, did you skip or reduce any of the acid containing ingredients?( oj, or pineapple sub, Brown sugar or honey? Etc Even the SUGGESTED subs have acid where needed. When baking soda ( or powder) are not fully utilized a metalic taste will occure. For me, I BOLD lable the best by date on everything I stock. It’s a bit of a pain when unloading groceries…BUT once you have ruined a batch of something you learn quick. I once ruined a double batch of cookies b/c the flour had expired by not too long past the date.
Hi! Was going to make these as 6 jumbo muffins! Do you think the cook time is same or similar to your jumbo blueberry muffins?! Thank you
Hi Hannah, yes! For jumbo muffins, bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-30 minutes or until the centers are set. Stick a toothpick in the center of a muffin to test for doneness.
I want to make these. I have an electric oven. I’m concerned about starting with the high heat. Not sure if the temperature will drop fast enough like with a gas oven. Any advice you could offer? Thanks.
Hi Carmen, the above method should work for any oven. As always, we recommend keeping an eye on the muffins as they bake, in case they do bake faster.
Do you prefer to use the light or dark brown in these muffins?
Hi Dottie, we’ve used both. Either works!
I’m getting ready to make these a second time. They were so good that they were gone in two days and there are only three members in my household. I’m getting ready to make a second time and I don’t have any apple and wanted to see if you think I could use pear instead?
Hi Clarissa, pears should work great!
We love, love these. Sometimes I use all pineapple, sometimes apple and pineapple and orange (today). Omg they are so good. Thank you for your wonderful recipes. Especially these!!
Love the recipe! It can replace my bran muffin recipe!
Similar to King Arthur’s…but BETTER. Love the additions of substitutions and baking tips!! For those who like to ” jump to recipe”, then ck out some reviews, I STRONGLY suggest scrolling back up to the blog portion and ck out her tips AND substitions. I now stock both crushed pineapple and pumpkin puree in my pantry as well as unsalted sun flower seeds [ which btw can also be a sub for the optional ground flax seed]
Love this site. This recipe. is a keeper. I have a covection oven Super great for roasted veggies NOT so easy for baked goods. But IF you also have a convection oven You NEED to make some changes to the baking directions.( It is not a flaw in the recipe…it’s the oven) 1) preheat the oven to 400 NOT 425. Then bake for 2 to 3 min. Turn heat down to 325 or 330 and check muffins at 16 min.
min. Add the note to your printed out recipe or in your cookbook for all baked items.
General rule of thumb for convection ovens is about 25° less heat and bakd times checked earlier
UPDATE: CORRECTION on baking times For ( MY ) CONVECTON these were the exact times that worked 400°
for 4 min ( NOT the 2 to 3 as I stated above.) Then down to 330 for 18 min. Which was for 16 muffins .I baked using weights given in grams and teaspoons as listed. This time I tried her. 2/3 C Crushed pineapple sub for 1 grated apple. I will keep that sub because I can keep the pineapple in my pantry & saves a little time as well..I have tested King Arthurs gluten free measure for measure twice ( 240 g for 2 cups) worked really well.
Hi Erica, thank you for giving our recipe a try. Usually when baking soda taste is quite strong, the baking soda is expired or is going bad.
Amazing recipe. I substituted zucchini in place of apple and added a couple of hand fulls of unsalted cranberry trail mix and made a loaf sprinkled with cinnamon sugar( Short on time) It was amazing and so are all your tips! tysm
I’ve made this several times and love it. Just wondering if I could replace vegetable oil with avocado oil?
Hi Chris, you can make that swap. The taste may be slightly different.
Can I use same weight whole wheat PASTRY flour?
Hi D, we haven’t tested this recipe with whole wheat pastry flour, and since it it finer than regular whole wheat flour, it would take some recipe testing to ensure the right amount (it may not be a 1:1 swap). If you do decide to do any experimenting, we’d love to know how it goes.