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
What do you think about the possibility of putting some oats in to these?
Hi Rex, That would require some testing. We’ve never added oats. If you soaked the oats, 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!
I love your recipes! What type of whole wheat flour do you use? I have whole wheat pastry flour, but wasn’t sure if that would be ok in this recipe or if there is one you recommend. Thank you!
Hi Marti, we usually just use regular whole wheat flour, but you should be able to use that pastry flour without any changes here.
I have made this recipe 3 times and probably again today ! Everyone loves them !! Thanks for sharing !!
This recipe looks delicious! I can’t do egg and was wondering if you thought flax egg as a replacement would hold up in this recipe?
Hi Chelsea! With three eggs, this may not be the best recipe to try egg replacements with, but let us know if you try anything.
I really like this recipe. I was thinking maybe you could let the ingredients sit in the fridge overnight to intensify. The flavor? Just omit the raisins, pecans, Apple, and carrots? And just mix those in in the morning? I have a lot of leftover boiled cider from this winter, so I wring out the apples of the liquid, and try to add back in the same amount in reduced apple cider. This is becoming one of my go-to baking sites, I really love the recipes and they seem to come out as expected.
Hi Sally can I use frozen orange juice or should it be straight from a bottle?
Hi Holly! Frozen orange juice is fine for these muffins.
Love this recipe! There’s a few things I left out since I didn’t have (flax, cranberries) and used half all purpose and half whole wheat bread flour since I was out of regular whole wheat. Turned out great, very moist!
Can I use all your muffin recipes to make muffin tops?
Hi Linda! We don’t have any experience baking muffin tops, can you usually use a standard muffin recipe, or does it need to be thicker? Let use know if you give it a try!
I bake these every Monday for my dad who is a senior. We love the fruit and vegetables in them and I usually add a little Turbinado sugar on top for an added crunch . These are the best Morning Glory muffins ever!
Morning Glory Muffins
So flavorful and fluffy!!
I have tried and loved so many of your recipes!! You listed milk as a sub for the OJ, could you use Greek yogurt instead? Trying to sneak protein in every chance I get!
Hi Lindsay, we haven’t tested it, but several readers have reported success with subbing Greek yogurt for the applesauce in these muffins. If you try it, please let us know how they turn out!
I would like to make this but my daughter is sensitive to honey, is there something else I can use as a substitute?
Hi Natalie, you can use more brown sugar, or try coconut sugar or pure maple syrup.
Do you peel the apple in the Morning Glory
muffin recipe?
Hi Linda, we usually do peel the apple, but you certainly don’t have to. Either way is fine!
Can you whiz both the carrots and apple in the food processor rather than using a box grater? Assume if one used this method you would whiz to a fine dice?
We’re sure you could, but it will be tricky to get the pieces to the right size. We do recommend sticking with a box grater, or some food processors have a shredding plate you can use as well. Let us know what you try!
I have weighred the carrots, then rough chopped, then pulsed fine- ish, (but not pureed). *(However, I do NOT pulse the apple.) It turnes iust fine. The apple turns out too thin and somewhat watery. BUT if you do not have a box shreddar you could THINish slice – then fine dice the apple.
I have used at least 15 of your recipes and every single one of them turned out fabulous. You are an exceptionally wonderful baker. Thank you so much for sharing your gift with us! I have a question about the morning glory muffins. If I replace the applesauce with crushed pineapple, do I drain the pineapple or use it in its juice? I assume I use it in its juice, but want to make sure. Thank you!
Hi Eileen, we would drain the crushed pineapple. Happy baking!
My cousin in Canada sent me a link to your Christmas Crinkle Cookies because I asked for the recipe. I made them and they turned out amazingly well. I love your recipes and will try some other recipes soon. Thank you so much, love your work!
Thank you so much, Maggie!
I don’t like cooking/baking with vegetable oil, canola oil or coconut oil. I have substituted apple sauce with vegetable oil in previous recipes, but you don’t recommend leaving out the oils.
Try using healthier oils like avocado or almond oil. Both are neutral tasting and now available at many stores.
Can you substitute butter for the oil in this recipe
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.
Can I use this recipe to make it a loaf instead of muffins?
Hi Barb, absolutely, you can bake this in a 9×5-inch 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. You can bake at 350 degrees for the entire time. Enjoy!
Can I make with almond flour??
We don’t recommend almond flour as it has very different baking properties and is not a 1:1 swap with al purpose flour. We haven’t tested it, but you might have success experimenting with a gluten-free all-purpose flour like Bob’s Red Mill or Cup4Cup. If you give anything a try, we’d love to know how it goes for you!
This recipe is regularly on repeat in my house. The best muffin recipe and turns out perfectly every time.
This recipe was so yummy! I did it all from scratch. Used homemade applesauce, the ground flaxseed, and the only change I did was using dried cherries instead of raisins as that’s what I had on hand.
Can I bake this in a loaf pan?
Hi Mombie, absolutely, you can bake this in a 9×5-inch 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. You can bake at 350 degrees for the entire time. Enjoy!
has anyone made these muffins without any sugar of any type? I would love to make these for my granddaughter but my daughter doesn’t want her to have any snacks with added sugar yet.
Hi Pam, 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.
These came out great! Grating the carrot and apple was a bit of a pain but the result was worth it. Only sub I made was unsweetened coconut flakes for pecans because it’s what I had. I made sure to measure everything using a kitchen scale and they came out with a nice moist and fluffy texture. I plan to make another batch with less sugar for my toddler but the amount of sugar in the recipe tasted great spread out over 16 muffins.
I left out the honey for my five year old and they were still delicious but just not so sweet. Next time, I would probably sub super ripe bananas and a small amount of maple syrup. We used pineapple in juice and added about a 1/3 cup of oats.
Would this be a good recipe to use freshly milled (whole bran) flour? Not sure if “whole grain” also implies whole bran.
Hi Sally! This recipe looks so delicious. I have leftover juice pulp made from carrots, apples, lemon and ginger that I’d like to incorporate into this recipe. Can I just sub 3 cups of juice pulp for the 2 cups of shredded carrot and 1 cup shredded apple? Will it be ok?
Hi Samantha, we haven’t tested the recipe that way, so are unsure of the results. Sorry we can’t be of more help here!
This looks fun. Do you have any ideas to use up some leftover boiled apple cider? I was thinking of adding in a tablespoon or two in substitution for equal weight applesauce?
Hi Chris! We haven’t tested adding boiled apple cider to these muffins, but you could also try adding some in the place of the orange juice. Sounds delicious. Let us know what you try!
I have been making these every week for about 4 months now, I make my father muffins every Monday morning to last the week, and these are by far the very best I have ever made. They are nutty and the texture is so earthy, I absolutely love them. 100/10! Thank you!
I love this recipe. So does my family,
Do you have the calories for these muffins? I appreciate it!
Thank you!
Hi Maria, 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