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
Hi Sally,
If I wanted to make these into lactation muffins, would you recommend adjusting the amount of flour to accommodate added brewerโs yeast?
Hi Molly! The muffinโs texture will change, but you can certainly give that a try. The muffins will be more dry. We do love these breakfast cookies and include lactation cookie instructions in the blog post.
Hello, when adding raisins to your Carrot Cake do you hydrate them first and what kind of raisins do you recommend?
Thank you
Hi Arlene, no need to hydrate them first. Any raisins are fine, I’m a personal fan of golden raisins if they’re available!
One thing my daughter in law and I agree upon are your recipes. I tried this muffin recipe, used my food processor to grate apple and carrots, walnuts as no pecans, fresh squeezed OJ and I must say these muffins are spectacular!! Can you determine a cooking time to make them in a jumbo muffin pan?
Hi Carolann! We’d use this morning glory muffin batter with the bake times and instructions from these jumbo blueberry muffins as a guide. Hope they’re a hit!
Hi Sally, I would like to make these higher in fiber. I would like to add bran to this recipe or would it be better just to add the carrot, apples and nuts to Healthy Bran Muffins? Thanks!
Hi Lori, bran can be a very drying ingredient, so we’d recommend following our bran muffins recipe instead and following the add-in recommendations in those recipe Notes. Enjoy!
I make these all the time. I am running low on WW flour but have WW pastry flour. can I use this instead or a mixture of both?
Hi Susan, We haven’t tested it but but you should be able to use that pastry flour without any changes here. Keep in mind it’s finer than regular whole wheat flour, so you may wish to use a mixture of the pastry and regular whole wheat to hold up to the moisture in these muffins. Let us know what you try!
Sally, have you ever made a morning glory loaf cake? I see where you make the muffins. I just watched “everything at the table” on YouTube the brunch episode and that is what she made. She didn’t leave a recipe which is fine because I trust yours more. I wasn’t sure how to adjust the muffin recipe. Thank you.
Hi Linda, 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!
10/10. Moist delicious feel good muffins!
I didnโt find these all that good!
Delicious. I used toasted, chopped almonds instead of pecans and Favorkit attachment for Kitchen Aid mixer to prepare carrots and apples.
Is there a suggested type of apples that should be used in a recipe like this one? Thanks!
Hi Emily! Here’s our post on the best apples for baking.
We love these muffins! I swapped nuts for shredded coconut to make them safe to send to school and they turned out great! Will definitely make again. Perfect morning snack for my preschoolers! But donโt forget to spray your liners. Learned that one the hard way!!
These muffins are worth the effort! I followed the recipe, using Sally’s suggestion of pineapple juice instead of orange juice. In addition, I substituted dried cranberries for raisins, since that is what I had on hand. Next time, I think I’ll take the suggestion of another commenter and use crushed pineapple. I love the flexibility of the recipe. Certainly one I will keep on repeat.
These are great!
I decided to save time I would make them like a sheet cake! Worked out fantastic. Cut in squares, freezing 1/2
Easy!!
These muffins are DELICIOUS!!!!! I made them exactly as written and will make again and again. I see where you can make a loaf instead of muffins which could be a nice change. Even so, a muffin is super easyโฆno cutting, perfect portion! Thanks Sally for the perfect muffin!