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.
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
- Bran Muffins
- Vanilla Almond Granola or Pumpkin Granola
- Chocolate Chip Baked Oatmeal Cups
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
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.
- 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
- 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.
- 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
Reader Comments & Reviews
I made these with King Arthur gluten free flour- wonderful- me picky grandsons love them!
These turned it very nice and moist. Everyone loved them!! Thanks for posting the recipe
Awesome recipe! Thank you Sally! My muffins came out moist and tender and they rose beautifully even with substitutions ( I subbed the whole wheat for spelt and omitted the brown sugar and replaced it 1/4 cup of lucuma powder and pure stevia ). You are a baking rockstar, all of the recipes I have tried from your site have been successful which does not happen often with recipes I try from blogs.
I adjusted a batch for my toddler, omitted the sugar and honey and subbed some chopped dates soaked in water (added enough date liquid to make up for the missing honey).
Both batches were delicious!
Little guy just ate 3 of his. Big hit!
Made these this weekend. I was able to stretch the recipe to 24 muffins. My only complaint is the lack of coconut in the recipe (but honestly that’s kind of on me for forgetting that I was going to put it in). I added less honey and more applesauce than recommended and I definitely see why more honey would be better. Regardless, this is a great recipe and it’s definitely my new go-to for morning glory muffins.
After mixing the batter for these I realized I somehow misplaced my muffin pan. To sub I made these in a 8×8 pan and cooked at 350 the whole time and they turned out fantastic! Great texture and flavor. Thanks for another knockout
These are amazing! I was looking for a muffin with some fiber for my 3 year old son who has tummy troubles and this is it! I substituted prune puree for the applesauce and they are still delicious. Very light/soft crumb with just the right amount of sweetness. Thank you!
These are amazing! The flavor of a carrot cake, but no guilt! I only had one full-sized muffin tin, so I did the rest of the batter in a mini muffin tin (425F for 5 minutes, 350F for 12 minutes and they tested done, yielded 12 additional mini muffins). I’m not a huge fan of the flavors of whole wheat flour or flax seed, but I can’t detect them at all in the finished product. These will be a great grab-and-go breakfast!
These are so good! Well worth the tiny bit of extra effort to prepare the ingredients. They even got the thumbs up from my 6- and 4-year-olds. And don’t leave out the orange zest/juice if you can help it – such a great background flavor! Thank you for this recipe!
I have small children, so we often make mini muffins. How would I change the cooking temperature/time to accommodate mini muffins? These were delicious!
Hi Courtney, For mini muffins, bake for 11-13 minutes at 350°F (177°C) the entire time or until a toothpick inserted in the center comes out clean.
I made these today, and have a question: I found with 2 tsp baking soda in them, there was a lingering taste from that which I didn’t prefer… I’m wondering if you know of any reason these wouldn’t work as well with both baking soda and baking powder, to lessen that soda-y taste. They’re a fairly involved recipe, so when I make them again, I want them to turn out well. I don’t want to sub in baking powder if there’s good reason to stick with the full amount of soda. What are your thoughts?
Hi Margo! 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– I fear with that much extra baking powder, the bitter aftertaste would be quite pungent.
These are delicious! I made them with dried cranberries instead of raisins and omitted the ground flax (just because I didn’t have any). The whole family loved them, including my 5 year old and 16 month old. I used an online recipe calorie counter, and with the modifications (cranberries instead of raisins and no ground flax seed), for a yield of 16 muffins, it came out to 218 calories per muffin, which is great!
Absolutely DELICIOUS!! I’m on a new healthy lifestyle diet and these fit the bill perfectly!!
I only have pears on hand can I use that instead of grated apple?
Love, love, love morning glory muffins. Thank you! This got me wondering. I made your baked oatmeal recipe – a huge hit with my family. Think there is a way to combine the two recipes – the flavors of morning glory muffins with baked oatmeal? Hmmm…
Hi Jen! You can leave out the berries in the baked oatmeal and add shredded carrots and apples, along with some ground ginger (there’s cinnamon already there!) and raisins (and/or pecans), too. Delicious. Enjoy!
I’d give 10 stars if I could. Sally, these are the BEST muffins I have ever had, from the texture, to the spices, to the subtle sweetness. These are definitely going to be a regular thing at my home from now on. Thank you so much for sharing!
Thanks for updating this post, Sally – the new pictures have wonderful lighting and colour, love it!
I made a halve recipe of these for my mealprep this week and got 9 muffins out of it. They taste great and keep well!
My ingredients variation: whole grain spelt flour instead of whole wheat, shredded pear for part of the shredded carrot (didn’t have enough carrots… I used a very firm variety of pears, amazing addition!), walnuts for pecans, freshly squeezed tangerine juice instead of orange juice (didn’t have any oranges).
A lot of the ingredients in the recipe are used as egg replacements, I would love to make a vegan version and I was wondering if you had any suggestions to replace the eggs or do you think it would be okay to just omit them completely?
Hi Aisha! I haven’t tested anything. I wouldn’t leave them out completely, so feel free to add more wet ingredients, flax eggs, or anything you’ve successfully used as a vegan egg replacer in other muffin recipes. (I’m not a pro at vegan baking, sorry!)
Hi Sally, made the Morning Glory Muffins, they are amazing. I prefer a dense muffin and these fit the bill, just the way I like them. Thank you so much for taking the time to post and share your recipes,. I love your site
Absolutely fantastic! Soft and tender, yet full of flavor.
DELISH! Easy to make and love your suggestions for substitutions! Family who I shared them with were very happy with their “Glorious Morning” muffin! Thanks Sally!
I made these yesterday to use up some extra fruits, veggies, and pantry ingredients. I love how versatile the recipe is and they are SO YUMMY! They may actually be better the next day. These are perfect for my super active husband, my busy toddler, and my snacky pregnant self. 🙂 Thanks Sally!
My insanely picky three year old called these “delicious” I am sooo thrilled.
First time making these and first time ever leaving a review. I followed your exact recipe did not substitute or added anything else. Muffins came out delicious, perfectly moist and not too sweet.
I have tried your recipe with gluten free flour (Cup 4 Cup or Bob’s Red Mill); for me they have always turned out perfect. It’s so great to have a hearty GF muffin since most of them out there aren’t great tasting and/or very expensive to buy. Thanks for another (updated) great recipe!
Absolutely love your recipes! I’d like to add oats in this. Do I soak it in milk like with your oat and blueberry muffin? Do I less use flour then?
Hi Liz! That would require some testing. I’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 me know if try anything!
This sounds super yummy! Can I substitute almond flour instead? What do you think would be the equivalent? Thanks! 🙂
Hi Jenna! The muffins will be too wet with almond flour. Instead, I recommend my blueberry almond power muffins.
These muffins are awesome. Great hit at the office new year’s eve party!
These are very good, Sally! I first saw these on your blog a few years ago and they’ve been on my list for that long. I finally baked them last night and we’ve already enjoyed half the batch! Thank you for your recipes. This one is a keeper.
Made these with all whole wheat flour for a church bake sale. Wasn’t thrilled with the consistency due to the wheat flour, but two ppl that bought some raved, one saying he’d buy me a drink if I made him a whole batch, lol! Happy that I could do something nice, I made some tonight, subbing in 1 cup white all purpose flour for one of the whole wheat cups. Still healthy, but I love the taste and consistency even more!