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!
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.
PrintMorning 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 (60g) 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.
Keywords: morning glory muffins
Thank you for the prompt response! I had no idea that baking soda could expire! I don’t see a date on mine and I just opened it. Maybe it’s just my post Covid taste buds messing me up again!
This is my first time making these muffins and they turned out awesome! The muffins were moist and delicious! I’m curious about the 2 tsp of baking soda vs other recipes where it’s 1tsp baking powder and 1 tsp of baking soda. I feel like I can taste the soda in these but my husband says he can’t.
★★★★★
Hi Tamara! Usually when baking soda taste is quite strong, the baking soda is expired or is going bad. That being said, you can definitely play around with this recipe and use some baking powder to replace the baking soda. Just remember that baking soda is 4x stronger than baking powder. And depending how much you replace– we fear the baking powder would leave an aftertaste.
This is my favorite muffin recipe because it is packed with so much flavor. I love that you have listed the many substitutions. I have made it first following your recipe and the second time omitting the apple and adding the crushed pineapple. The pineapple adds more moisture. I was surprised how moist this muffin was with just whole wheat flour, but very happy with the result. I also did not have ginger so I used cloves instead. This is a muffin recipe that I will keep on making. Thank you for so many great recipes. I am addicted to all your recipes because they all turn out perfectly. I only go to your recipes now. One stop Baking. Thanks.
OMG! No Fail Morning Glory Muffins!
I have always loved morning glory muffins when purchasing at my favorite coffee place. I have been looking for a go to breakfast option for quite sometime and was not really satisfied with store bought options. I realized I did not have enough carrots so I halfed the recipe. Also, I didn’t have ground ginger so I used candied ginger and grated it. It so delicious, moist and satisfying to have.
Thank you Sally!
★★★★★
Love this recipe! The muffins are perfect every time. May be my oven but once the temp is turned down to 350 they are baked in 12-13 minutes.
★★★★★
Made as loaf, then have a question:
I’ve made these once as muffins, and once as a loaf. I liked the loaf version, but I had trouble getting the timing and temperature right. I started at 350, but the outsides were cooking too quickly so I dropped it to 325 and ultimately 300. In the end the outside 1/6 of an inch was a little overdone, and a little bit in the middle – about 1″ I think – was underdone.
I have a question before making it next: I’d like more flavor of coconut, and ideally more pineapple too. I decreased pecans and raisins and added 1/2 cup of coconut, but I couldn’t taste it. I used crushed pineapple instead of 1 cup of carrots, and pineapple juice, and couldn’t tast that either. Could I go up to 1 cup of coconut without changing anything else? Could I go up to 3 Tbsps of pineapple juice? And is there a way to get a full cup of pineapple? If I need to change more things I will. I’d happily lose the pecans altogether, and raisins too if I need to.
Hi Ellen, you can replace the pecans and raisins with 1 cup of coconut. You can replace the 1 cup of shredded apple with 2/3 cup canned crushed pineapple, and then replace the 1/3 cup of applesauce with crushed pineapple. That should help those 2 flavors shine through a bit more. As for the loaf, we recommend keeping the temperature at 350 to ensure it bakes through. If you find the edges begin to brown too quickly, you can tent the pan with aluminum foil. That will prevent the edges from over browning while allowing the middle to continue baking through. Hope this helps for next time!
Thank you for the reply! Is there a reason you would replace the apple instead of carrots with pineapple?
These muffins are incredible. They are extremely versatile, you can add and subtract things to them very easily, and it does not compromise the texture. I substituted half the brown sugar with coconut sugar, and they came out perfect. I also added a can of crushed pineapple. I love all the healthy ingredients.
Wow. I don’t normally go for muffins, as they are usually a small piece of cake. Just have cake! These are not cake, these are energy food packed with flavor and perfect for someone in a rush. That taste amazing. Quite honestly one of the tastiest baked goods I’ve tasted. Bloom the raisins in your juice for something even your picky eaters will approve of. Thanks for the recipe! I will be making a nice big batch weekly for a friend who was tired of paying $4 each for these.
★★★★★
These look great, but I’d like to make them sugar free. Would that work and, if so, would I need to make any other changes to the recipe? Thanks
Hi Hannah, the sugar plays an important role in the taste, texture, and structure of these muffins. We do not recommend leaving it out completely. See blog post above for a few substitution options for both the brown sugar and honey.
Turned out tasty but how can I get muffins that don’t stick to the paper cups? I did use spray on them. Do they need to cool more?
★★★★
Hi Judith! We recommend using high quality grease-proof liners. They make a big difference. We love Paper Chef brand parchment baking cups. Letting the muffins cool completely will also help.
Wow. I have never baked healthy muffins. These are incredible and approved by my nutritionist! I used cranberries instead of raisins but otherwise followed everything exactly. Will be making these many more times.
Thank you for another delicious recipe.
★★★★★
Make and freeze . Allergic to cinnamon so I use cardamom. Love the choices of substitutions!
These muffins are delicious!
Also how do I know if the recipe calls for fan bake or not fan bake as the temperature varies by 20C for my oven.
Hi Sue! All of the recipes on this site are written for conventional settings (not fan).
As always a Great Sally Muffin! I used crushed pineapple instead of applesauce and added 3 T unsweetened coconut flakes. Did not have any flax. My favorite Morning Glory muffin recipe!
★★★★★
First time cook. Do the apples need to be peeled BEFORE grating?
Hi Deb! We usually do, but you certainly don’t have to. Either way is fine!
I so want these to turn out, they look soo delicious!
Questions: Does the baking time change if all i have are non-stick muffin tins EVEN though I am using a paper liner? And I noticed you mentioned do not leave out BUTTER, but after putting together, I noticed in ingredient list , it listed oils, I used canola oil-was that interchangeable for the melted butter? My batter wasn’t as thick as your in video, & I carefully measured flour by spooning into 1 cup & leveling with knife. ..just wondering.
Hi Deb, the baking time doesn’t change for non-stick pans. Oil is best here, but melted butter can also be used if desired.
These were not my favorite. I was so surprised given I have tried and loved SO many of Sally’s recipes. I bake using gram measurements and followed the recipe without any substitutions. Perhaps using some substitutions would improve it for my family and I.
★★
Hi Julia, thank you so much for giving these muffins a try. How was the texture of the muffin? If you wish to try again to achieve a different taste, using some of the substitutions listed in the post could definitely help. Let us know if you do!
By far the very best muffins I’ve ever made.
★★★★★
I just love the flexibility of this recipe– I can make these week after week with different little alterations and I never get tired of having them for breakfast! Today I’m celebrating fall by using pumpkin puree instead of applesauce and dried cranberries instead of raisins. Thanks so much for the recipe!
★★★★★
Muffin recipe turned out great. Can i make this as a quick bread, using a 9×5 loaf pan. I realize the bake time will be longer…..@ 350° instead of higher initial bake temp
★★★★★
Hi GMJ, 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.
Turned out delicious! Will definitely make again this fall!
★★★★★
Wow these are so good!! Just made these and love them so much, I know they will be regularly in our breakfast rotation. We are trying to reduce sugar as much as possible in our household so I skipped the brown sugar and added in 2 smashed bananas as well and they still turned out fantastic.
★★★★★
Hi
Can I use an all bran cereal in this muffin recipe? Would I be able to use a cup in place of 1 cup of the flour?
Hi Tricia, we haven’t tried that substitution, but let us know if you do! Alternatively, you may enjoy our Bran Muffin recipe!
I really like these muffins a lot. I have one with a 1/2 cup coffee an hour before I go out for a morning run and it gives me just the right amount of energy to keep me going for a good 4 mile run. I have a bunch in my freezer and I’ll take one out at night to thaw for the next morning. Great energy for on the go. Thanks
Do you have a calorie count (carbs, fat, protein) for these?
Hi Rachel, 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
I have made them almost every week since I discovered them. I take them around to my neighbors on some mornings and now my daughter and Grands up in Sonoma ask me if I broughrvsome every time I visit. Best breakfast muffin ever!
★★★★★
This is it. This is my favorite muffin recipe. The grating takes some time, but it is so worth it for how moist and delicious they turn out. Got some baking now with dried apricots and I’m pumped.
★★★★★
PS: Also used olive oil, as part of a heart healthy substitution. With all the other flavors, can’t tell the difference!
Crazy moist and delicious. I accidentally cooked the second set of muffins at the higher temperature for about 10 extra minutes, and they still taste great. I followed the recipe exactly, including the zest and flaxseed. So worth the prep time, which is more than most muffin recipes.
★★★★★
This is a great recipe! Today I made these muffins with Better Batter Gluten Free All Purpose Flour and they turned out perfectly.
★★★★★
I love these muffins and echo Tara’s sentiments. I often try with a variety of dried fruit, along with different ratios of grated carrot and zucchini. They don’t last long and perfect every time. This week I plan to be entering them in our county fair, too!
★★★★★