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
Hi! I adore this recipe – definitely a go-to breakfast for us. One quick question – may I mix the batter the night before and then scoop/bake them off in the morning?
Hi AP, 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!
This is a hit with my girls. Thank you. I’m wondering about substituting oats for some of the flour. What are your thoughts?
Hi Jennifer! That would require some testing. We’ve never added oats. If soaking, you’d have to reduce another wet ingredient. If using as dry, you’d have to *slightly* reduce the flour and/or flax. Let us know if try anything!
Absolutely brilliant recipe! Easy to substitute different nuts and works really well with UK ingredients.
I used standard UK muffin cases and the second bake was 13 minutes so our cases may be slightly smaller.
Highly recommended for snacks, puddings or a toddler breakfast.
Simple morning glory muffins from Sally’s Baking Addiction were a pleasant addition to my breakfast routine when I recently tried them! Carrots, apples, and nuts combined created a tasty and moist treat. For an extra protein boost, I added Kodiak Cakes mix (https://kodiakcakes.com) to the batter, and it worked out beautifully. I appreciate you sharing this healthy and tasty muffin recipe; it has quickly become a family favorite!
This recipe came out perfect – muffins have a crunchy exterior and moist interior! Will definitely be throwing these into my muffin rotation.
I’ve made many of your recipes but hadn’t made these until today. Love this type of recipe for how easy it is to sub ingredients as needed. I didn’t have enough carrots so I used shredded zucchini as well, maple syrup for the honey, mashed banana for the applesauce & buttermilk instead of the juice. Turned out beautifully! Thanks again for such a great resource for recipes
Hi! Any suggestions on baking times with mini muffin tins? I would like to make them bite size for my toddler.
Hi Susi, If making these in a mini muffin pan, bake 13–14 minutes total at 350°F (177°C) the whole time.
Just wanted to give a heads up that this recipe worked great with King Arthur gluten free measure for measure flour (I weighed it for the most accuracy). Baked just as stated and the texture was perfect!
These were delicious – I used my food processor to grate the carrots and an unpeeled, cored apple (I used the grated apple in place of applesauce.
These turned out so good! I subbed flaxseed for chia seeds because it’s what I had on hand, I added shredded Coconut in place of some of the carrot because I underestimated how many carrots I needed, subbed dried cranberries in place of raisins, and I forgot to add the baking soda. But they still turned out really good! Very forgiving recipe is an understatement
I will say I added baking soda once I realized before I cooked the last few and the ones with baking soda taste normal but the ones that didn’t get it taste eggy. So try not to forget the baking soda lol
I don’t have any whole wheat flour. Can I use all purpose flour?
Definitely!
Have done this recipe twice and it came out amazing both times. Second time used egg substitute and still turned out great
Can I use my muffin top pans for this recipe? If so, how long and what temp to bake at. Thank you!
We haven’t tested it, Nancy, but let us know how it goes if you do!
I was wondering what whole wheat flour you used because I’ve noticed different protein contents on storebrand whole wheat flour or King Arthur
Hi Jessica, we typically bake with King Arthur whole wheat flour, but you can use any brand you prefer.
Hi Sally, could I use whole flaxseed instead of ground?
Hi Annie, absolutely. You may want to decrease the amount a bit, but that’s up to your personal preferences. Let us know how it goes!
These are so yummy and healthy.
Hello!
I’m switching from regular to jumbo muffins/cupcakes. Any tips for bake temp/time?
Also, we live at high altitude. A couple of tips for your high altitude bakers: I use Hungarian High Altitude Flour, and although there is high altitude baking powder, I get better results when I double it.
Hi Jorjean, For jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
Can’t beat a delicious Morning Glory. 🙂 thanks Sally. I added about 1/2C coconut. Is there a reason coconut isn’t in your recipe? Otherwise I made it as written and love it.
Hi Andrea, We have replaced the pecans and raisins with 1 cup of coconut.
No applesauce so used mashed banana. Muffins turned out great.
I am confused and need your advice. The recipe calls for 2 cups of whole wheat flour (260 grams). I am using King Arthur whole wheat flour and their website shows 113 grams weight for 1 cup of wheat flour. I spooned, leveled, and weighed a cup and it weighed 126 grams. If I go by weight it will not be 2 cups. Should I use the measured amount of the flour or the weight of the flour for this recipe. I don’t want to proceed without knowing for fear of wasting the sheer amount of the other ingredients.
Thank you . . . Mike
Hi Mike, weight is always the most accurate measurement, so we’d measure out 260g of whole wheat flour and use that. Hope you enjoy the muffins!
This recipe is fantastic! I made it with fresh milled whole wheat einkorn flour and followed the recipe to the letter. They had a beautiful texture and a delicious bright flavor. Not to mention they are more filling and substantial than the average muffin. They were a huge hit with everyone in my family. Even members who didn’t expect to like them. Thanks!
This was my first time making these muffins, and they were absolutely delicious. I used only 2 eggs and added 1/3 cup shredded coconut but otherwise followed your recipe. The recipe yielded 13 regular sized muffins baked to perfection for 20 minutes total in my oven. They were light, moist and perfectly spiced. The amount of sweetener is just right. With so many available recipes now on the internet, I invariably come back to your site as “home base” for recipes that give consistently yummy results.
Very tasty! Made them once exactly as described and once with small frozen berries because I didn’t have apple. Wonderful recipe!
Thank you for the perfect muffin recipe! I substituted yoghurt for applesauce and they still turned out beautifully. When in doubt I always come back to your website for perfect recipes every time!
Having issues with paper sticking to the muffin. Any suggestions?
Let the muffins cool a bit longer, and try again. Sometimes the muffins are just too warm and will stick. If it keeps happening, try switching to parchment paper liners if you try these (or any muffins) again. I like the ones by the brand Paper Chef.
Give the muffin liner a slight spritz with nonstick cooking spray. Then they peel off beautifully!
The Supreme Morning Glory Muffin-I’ll
use this recipe from now on. I added some coconut and shared with three people at work-all of whom loved them. They are so moist and flavorful. Thank you for the recipe!
Hi! Wondering if you can cut out the sugar (or coconut sugar) all together and instead just use a combo of maple syrup and honey? Thank you!
Hi Lauren, we don’t recommend cutting out the sugar completely, but you can use the coconut sugar in place of the brown sugar.
I used maple syrup and honey, and they came out beautifully!
Very good! I added pineapple with the golden raisins. These will be made here again!
I followed the instructions for the baking, 5 mins. 425, 18 mins at 350. I had to take them out before because they looked very brown, with a burnt smell. I will try a second time.
After reading the rave reviews, I was disappointed that my family found these muffins “too spicy”. I believe they are tasting the ginger. Have you tried the recipe with cinnamon only? Or substitute cloves for ginger? I made the recipe exactly as written with no subsitutions.
Hi Chris! You can leave out the ginger if you prefer.