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, flax, 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 flax 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. 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 Oatmeal Cups
- Chocolate Banana Muffins
- Bran Muffins
- Vanilla Almond Granola or Pumpkin Granola
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, flax, 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 (spoon & 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 flax 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
- 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
Fantastically delicious! I’m wondering how I could pull off making it as a loaf instead? Is this something anyone has tried?
★★★★★
Delicious! This recipe is a keeper – no need to say anything more.
★★★★★
Fabulous recipe. 425 for 5 minutes is key. Timing is perfect. I substituted 3T ground chia for flax soaked for 20 minutes in 9T water. Replaced 1 c flour with 1/2c oat bran and 1/2c almond flour. Added 1/8 tsp allspice, cloves, cardemon and grated nutmeg. Added 1/2c unsweetened dessicated coconut.
★★★★★
I have made it exactly as above and it was awesome. I have also made this for highly allergic friends who are gluten-free, dairy/egg-free, and can’t have regular sugar either. I adapted it and it was delicious. This is what I did:
-replaced flour with 1/2c quinoa flour and the rest Gluten Free oatmeal
-replaced eggs with banana & water-soaked chia seeds
-replaced sugar with maple syrup.
It held together and was still super tasty! Everyone was impressed. Thank you!
★★★★★
Can I use this recipe to make mini muffins? do I fill to top? how long do I bake them? Do you have mini muffin recipes I can try? I also want to try your lemon blueberry cake. Thank you. Beth Hutcheson
Absolutely! See step 3. Fill to the top. Here are all of my muffin recipes and most include mini muffin instructions, too!
I just made these using zucchini and bananas instead of carrots and apples, because that’s what I had, and they came out fantastic! Also threw in some chopped candied ginger, mmmm that really added a nice punch of flavor. I’ve always struggled with flat muffins, but the higher temp at the beginning made them nice and rounded. Thanks for a really great recipe!!
★★★★★
An amazing recipe! I made these gluten free with 3/4 gluten free flour blend (Doves Farm for anyone in the UK) and 1/4 buckwheat flour. They turned out delicious! Thank you very much!
★★★★★
I’ve been trying different healthy muffin and cookie recipes every week and these are the BEST! No matter how I change them up with her variations they are always superb. Never dense or dry, they are always moist and flavorful. I love that most use whole wheat flour and oatmeal and not much sugar if any. I think Sally’s idea of baking them for 5 min.on 425 is genius . The only request I have is to keep the recipes coming. And maybe how to bake them in a big muffin pan.
★★★★★
Excellent! I soaked my raisins in hot water before baking and they were super moist. I used unsweet coconut flakes in place of nuts.
★★★★★
This recipe is so moist and delicious!
★★★★★
These are absolutely the very best muffins ever!! I have made them 4 times before and currently have some in the oven right now. Everything Sally puts out has been incredible, if you have not tried one of her recipes you NEED to.
★★★★★
So good! Baking instructions were on point.
★★★★★
Yummy! I only had regular applesauce so I cut 1/4 of sugar. Used dried cranberries and chopped walnuts. My muffin tins are rather large, so it made 12 nice size muffins. These are so good!
★★★★★
I was able to adapt this recipe to my low sugar vegan diet and it came out so good!! I swapped the 1/3 c applesauce for 1/3 cup of coconut cream, then used 3 tablespoons of melted vegan butter for the rest of the oil. I also substituted lemon for the orange zest and juice and used 1/4 c brown sugar and 3 tablespoons of maple syrup for the sugar component. For the eggs I used 3 tablespoons of ground flax mixed with 9 tablespoons of warm water. Amazing!!!
★★★★★
these are perfect! i can go 1/4 cup less on brown sugar for my sweetness preference and did the sub for zucchini over apple.
★★★★★
Delicious. I left out the raisins because I thought the muffins would be sweet enough without them, but I think you could go either way (I’m making them with raisins next time). The hardest part of the whole recipe was the “cool until ready to eat” part. Thank you!
Amazing recipe! These muffins are super moist, fluffy, and not overly sweet – the perfect compliment to a cup of coffee or tea! Only changes I made was to sub out organic carrot juice instead of orange juice (it’s what I had left over from a different recipe); instead of pecans I added unsweetened coconut flakes (wanted to share with my young kiddos so left the nuts out), used the zest of a clementine instead of an orange, loved it and will certainly make these again real soon! Thanks, Sally!!
★★★★★
This recipe looks absolutely delicious! However, before I make it I have a question. I have never used Flaxseed before. Should I use a coarse flaxseed grind or a Flaxseed meal?
Thank you for your help and thank you for all of your wonderful recipes!
Becky
★★★★★
Hi Becky Ann, ground flax/flaxseed meal is what you’re looking for. It’s an optional ingredient, so feel free to leave it out.
This was my first recipe from your site. Had to make a couple of small substitutions due to quarantine limitations (made it with a mix of spelt, rye and buckwheat instead of wholemeal flour) and I impulsively threw in a spoon of peanut butter and some chia seeds as well for some extra goodness. I also highly recommend sprinkling the tops with some brown sugar, oats and cinnamon before they go into the oven.
They are soooooo good. I have had a muffin for breakfast every morning this week. They fill me up and I don’t feel hungry until lunch because they’re packed with fruit, nuts and seeds. I can’t wait to make them again.
★★★★★
Fabulous. Very flavourful muffin, like spice coffee cake. I substituted the carrots and grated apples with raspberries and blueberries. I will definitely make these again
★★★★★
I made these for the first time and they’re delicious! I think 18 minutes on 350 is too long and made them a little dry but my oven may be a little off. I really like that they’re not overly sweet and there is so much fiber from the whole wheat flour and the ground flax seed.
★★★★★
I have been looking for a recipe for this as this is perfect! I made and my family enjoyed it very much! Thank you for sharing this recipe.
★★★★★
This will have to wait til next week. I just made a big batch of Orange-Cranberry-Chocolate Chip muffins. They contain all that stuff many people want to leave out or substitute, like butter, flour, eggs, milk, brown and white sugar, fresh and concentrated OJ, zest of one large California orange, REAL dark chocolate chips, cocoa etc lol. Oh yes and bran, mustn’t forget the fibre lol. One of those with your morning coffee and you’re good to go!
Delicious! and perfect to start the day.
★★★★★
These look delicious! Have you ever put zucchini in as well?
Oh my glory! I made these (with a couple omissions-which were optional) & the addition of crushed pineapple. These are divine! Seriously! I love the heartiness that the whole wheat flour gives with and the different textures. You definitely don’t feel bad eating these guys (Unless you have 5 in one sitting! Which I didn’t!)!! Thank you, thank you, thank you for such a great recipe! <3
★★★★★
First time using one of your recipes. Substituted all purpose flour. Also didn’t have raisins or cranberries. Sadly, no one here likes nuts but me. I am really loving the smell of them baking! Unfortunately, I didn’t watch them closely enough and the burnt on the bottom and a bit underdone in the center. I have a lot of carrots and apples. Will try again
Made these in mini muffin form, and my family LOVES them. There is so much flavor in them, and they are great breakfast muffins, or guilt-free treats during the day. I added a little more cinnamon to the batter than stated, and added a bit of nutmeg as well. Also, I substituted walnuts for the pecans. Otherwise I followed the recipe as it is stated.
Will DEFINITELY be making these again!
I wish I could post a picture of how they came out!
Hi Sally,
My sisters, mom and I LOVE your recipes! Thank you!! I am wanting to add some whole old fashioned oats to this recipe, and don’t care for pecans in my muffins–could I just do a straight substitution? Or should I also sub a little flower for oats as well?
Thank you 🙂
P.S. Congrats on your little one on the way!
Hi Lily, you can certainly try leaving out the nuts and replacing with oats. I haven’t tested the recipe this way, so I’m uncertain of the exact results. You may enjoy my oatmeal muffins instead!
Thanks, Sally! I replaced the nuts with oats and they are so delicious! I didn’t end up replacing any flour. These will definitely be a repeat recipe for me. Your oatmeal muffins look great too!
★★★★★
These were delicious without being sickening sweet. The texture of all the goodies in them make them wonderful for breakfast or with a cup of afternoon coffee. They came out of my sprayed muffin tins without any trouble and the rise on the top was picture perfect! I added coconut but otherwise followed the recipe. Great way to use up carrots in the fridge!
★★★★★