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.
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 (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
- 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
These muffins are amazing. I’ve made them several times with different combinations of carrots, apples, zucchini and pineapple and every time they are moist and delicious. They don’t last long around our house. Today I left out the sugar but added a bit more honey instead of some of the juice and it worked just fine – absolutely sweet enough and packed with veggies. Delicious!
★★★★★
Can I make mini muffins using this recipe? If so, at what temperatures?
Hi Candice, for mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.
I love your recipes but got sick and had to change my diet. If you can do very low carb desserts I would be so happy
great recipe, thank you. how do you adjust the baking time if baking in jumbo muffin pans?
Hi MH, you can make this batter in jumbo muffin pans, following the bake time and directions from these jumbo blueberry muffins as a guide. Glad you enjoyed these!
I have a toddler who is a very picky eater and he loves these muffins, so much so that I make half a batch just about every week. Because I half the recipe, my measuring isn’t always super precise but the muffins always turn out great. Ands it’s great to be able to substitute ingredients based on what I have on hand. One of our favorite variations is using maple syrup instead of honey and Simply orange-mango for the juice.
★★★★★
I loved this recipe so much! They were truly perfect. The only tweak was adding 1/3 shredded unsweetened coconut. I’m sure they would have been equally delicious without, just a personal preference. I doubled the recipe as they’re a bit of a hassle to make with all the grating and zesting involved. I love having extra for the freezer. My toddler and husband devoured them, as did I! Will be adding to my regular rotation.
★★★★★
I tweaked your delicious recipe a little by using 1 cup ww flour and 1/2 C almond flour and 1/2 C garbanzo flour and sub crush pineapple and juice for apple and OJ. Plus added 1/4 cup shred coconut. Turned out delish!
★★★★★
Great recipe! Has anyone tried adding some cocoa powder? I dream of a chocolate version of morning glory muffins, but maybe that’s asking too much!
★★★★★
Hi Janet, we’re so glad you enjoy these! We haven’t tested a version with cocoa powder; unfortunately, it’s not always a 1:1 swap with flour and can be a bit drying, but if you decide to do any experimenting, please do let us know how it goes!
I have made a version of these for years . These have way less oil. I add unsweetened coconut as well. Delicious.
★★★★★
Can bake this in a loaf pan?
Hi Tammy, 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.
I am a newbie at making muffins. How firmly should I pack into measuring cups ingredients like shredded carrots, shredded apples, and raisins?
Hi Debbie, for those ingredients, simply scoop or pour them into a dry measuring cup (no need to pack tightly as you would brown sugar). Hope you enjoy the muffins! (PS: you may find this post on how to properly measure baking ingredients as a helpful resource, too.)
How fine do you grate carrots and apples?
Hi Roberta! We use the larger grating side on our OXO box grater.
Delicious! I’ve made these last night and have already eaten 4. I used apple cider rather than orange juice, which tasted great. The pecans (from the recipe) were a nice addition since they added texture. I’ll make these again for sure
★★★★★
Muffins were delicious…used pineapple instead of apple & coconut sugar
These muffins were so tasty. My only issue is that they fell apart so easily, crumbling away as we ate them. What did I do wrong
★★★★
I tried giving this recipe 5 stars
but couldn’t get the above stars to work. These were easy to make and delicious. Had a hard time just eating 1 at a time
★★★★★
I’ve been making these muffins for three weeks now, they’re fantastic! I didn’t have any apple sauce last time, and used two aged bananas, and now my husband is eating them all! This is a seriously good recipe. Thank you so much!
★★★★★
I made Morning Glory Muffins this morning because I wanted something “good” form me on which I could slather PB. Mmmmmmm good. Since it was a spur of the moment thing, I used oatmeal, not flax; banana, not applesauce; craisins instead of raisins, and candied pecans that I made last week and needed to stop munching on them. Love the versatility of this muffin. Thanks Sally and Co.
Your post makes me happy, I can relate and laughed out loud when reading it!
I think this recipe was great and easy to follow! I used whole flaxseed which added a nice little crunch and some fresh nutmeg, but otherwise followed the recipe as written. They are not my type of muffin, but my dad absolutely raved about them (which is good, since they were for his birthday haha).
★★★★★
So delicious! I have literally searched all over for a good one, and this is honestly the best one!
★★★★★
These turned out great! Nice texture and taste, perfect for a healthier breakfast muffin. I calculated the calories for 16 muffins and it is about 210 which is good. I only made one substitution, I used ground chia seed instead of ground flas seed because it was all I had. Ground chia is not as nutty as flax, but it has about twice the fiber per tablespoon. These muffins with ground chia are 4 grams of fiber. Taste great. This recipe is a keeper!
★★★★★
Turned out awsome ! I have used Hemp seeds in place of Flax seed, & 227g King Arthur’s WHITE whole wheat flour. ( which is still 100% whole wheat flour…NOT bleached. . Wheat grows in either a darker brownish color OR a lighter pale tan color. Both are whole wheat, no stripping of the whole grains in the white whole wheat version. But a milder taste, VERY similar to All Purpose.flours..although the weight varies per cup) I have also used pumpkin pie spice in ground ginger when I did not have any on hand. It has ginger in the blend. Now I use both ginger and pumpkin pie spice(1/2 t. each) on many occasions. The rest is the same..Love this updated recipe with detailed subs. I often get a jump start on making many baked items by carefulky weighing or measuring all my dry ingredients, then placing them in a zip lock bag. It saves a step later. BUT be SURE to label what it us for AND date the bag with the EARLIEST expiration date of flour and baking soda.
As written this is awsome. I may try more subs in the future if needed.
After many years of baking, I have learned that weighing ingredients is far more successful than cup measuring…even when spooned and leveling off.
★★★★★
JUST A TIP for having problems with muffins sticking to muffin cups OR liners. I spay muffins cups unlined with baking spray that also has flour in it. ( but NOT for G.F muffins …reg spray is fine) .Another professional site advises spraying liners LIGHTLY if using those. But best muffin cups i have ever used is USA muffin cup pan Sally site has a link to amazon that limks to that choice, just scroll up and tap the link. Yes, her team gets some kind of credit…BUT it does not cost you any more money.. I personally like giving back to my fav sites…especially when it does not cost me a dime. Either way USA baking equipment items are the best I have tried in 25 yrs of baking.. { even though they are non stick….I still spray muffin cups and cake pans with BAKING spray}
I made these morning glories twice now, and they are a hit! Moist delicious and nutritious!! Thank you.
★★★★★
My finicky husband LOVED! He said very tasty and moist. I did add a little bran to the mix (shorted a bit of the flax seed).
★★★★★
My husband is addicted to these. I have made a new batch every 2 weeks without fail for the last two years. He has one for breakfast every day.
★★★★★
Hi Sally. Can I bake these as a loaf instead of muffins?
Hi Nadine, 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.
I keep these on hand at all times! It’s just my husband and me at home now so I keep half of them out and freeze the other half. We warm them up and enjoy them with our coffee almost every morning! It’s a team process when making them: he grates the carrots and apples and I do the rest! Love, love, love this recipe!
Very good recipe. Followed as best I could. I didn’t have any flax so omitted and only had craisins so used those. Cooked on 2 racks in my convection oven. Cooked 3-4 minutes faster than standard bake setting. Took a while to make with all the prep and a lot of clean up but I think they are worth it. Will be making again
★★★★★
Do you have to use wheat flour?
Hi Jane, you can use the same amount of all-purpose flour instead.
Do I need to adjust any liquid in order to add shredded coconut.
Hi Lauren, no need to, simply replace the pecans or raisins with shredded coconut.
I have used this recipe for years. Forgot the apple sauce once but still turned it great!! Various fruits used are still delicious.
So moist and flavorful. I loved them!! Thank you for your wonderful recipes!
★★★★★
Just made and they are wonderful! Used walnut oil instead of veg oil, reduced sugar cranberries, and maple syrup instead of honey. Added chopped walnuts and a dash of cinnamon/sugar on top before baking. I thought the batter tasted too sweet but the baked muffin was perfect. Tall, moist muffins. Calculated nutrition at 158 calories, 7.9 grams fat, 15 net carbs, per muffin. Really can’t beat that!
★★★★★