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 (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 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.
Love these muffins! I’ve made them plenty of times before, but today I realized halfway through that I wouldn’t have enough carrots/apple/banana for the 3 total cups of shredded or mashed fruit. The only thing I had in a pinch to substitute was that sliceable canned cranberry jelly. I mashed it up with a fork and used a cup of that, in place of a cup of shredded apple. Surprisingly, it worked, and the cranberry flavor is delicious!
Can I substitute 1 cup of oatmeal for 1 cup of flour?
Hi Carole, it would take a bit of recipe testing to ensure results, as oatmeal absorbs wet ingredients differently than whole wheat flour. You may like these blueberry oatmeal muffins instead.
Why is the orange juice crossed out on the recipe? Should I not use it?
Hi Linda, the recipe card has a feature that lets you cross off the ingredients as you use them. If the orange juice is showing as crossed out, it’s likely you just accidentally clicked on it!
Could this recipe be used to make a small loaf (or two) rather than muffins?
Hi Melissa, 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!
First off thank you for sharing this lovely recipe! I have been wanting a good morning muffin ever since my favorite coffee shop stopped selling them. Next time I make this I will leave out the orange zest and add more pecans! ☺️
I really enjoy these muffins, and I really love your harvest spice bread in muffin form. What changes would you recommend in order to incorporate pumpkin into this recipe? Thanks!
Hi Courtney, So glad you love these! You can use canned pumpkin in place of the applesauce.
I don’t have apple sauce or plain yogurt what can I add in its place?
Hi Rebecca, you can replace the applesauce with melted butter or more oil, apple butter, mashed banana, canned crushed pineapple, or pumpkin puree.
Great recipes!!
This is my favorite muffin recipe by far. I have made it countless times and I thought I had made every substitution possible. I always use 1/2 cup plain yogurt in place of the honey and applesauce. Usually I don’t have oranges or orange juice on hand, and I generally leave it out. This time I remembered and old (Moosewood??) banana bread recipe that had coffee and lemon zest in it. I zested a lemon in and added 1/3 cup coffee instead of the OJ and zest. Wow. May be worth a try.
I love this recipe! It’s so versatile. Last week I made beet, apple, carrot, ginger juice and had about 2 cups of pulp. I tossed that in instead of the grated carrot/apple – it was wonderful! I’ve also subbed some of the flour (1/2 cup) with protein powder, added mashed banana and yogurt – always a hit.
For high altitude: bake at 450 for 5 min, then drop to 375 for 14 minutes. Perfect.
Hi there. My family and I love this recipe so much. They are truly the best breakfast muffins! Quick question, can I bake this batter in a loaf pan instead? If so, what would the baking time and oven temps be? Thanks.
Hi Ellie, 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!
This is a great recipe and well worth the effort. The whole family loves them and they’re a healthy snack or breakfast for my five-year-old granddaughter.
I made this recipe with so many substitutions and it came out perfectly. Convinced you can’t mess this up!!
Omitted all honey and orange zest
Swapped milk for oj
Used olive oil in place of veg oil
Used 1 1/3 very chunky applesauce
Omitted apple grated
Subbed zucchini for carrot
Omitted pecans
Swapped cranberries for raisins
The muffins seemed to never cook thoroughly
Hi Pat, how long did you bake the muffins for? Every oven can be a bit different, so it’s okay if yours take a few minutes longer than expected. You can use a toothpick to test for doneness.
Hi Sally and team. 🙂 I’m so excited to make this recipe for quick, tasty, wholesome breakfasts this school year. I will make it as directed next week. I can’t help but wonder though… How might one add pineapple (say, slivers or tidbits) to these muffins? If fine enough, would it replace the apple if processed fine enough? Or, might it replace raisins (they are dry, and eek, pineapple is not)? I have had some wonderful carrot cakes in the past with pineapple right in the cake, so I’m wondering if I might replicate those flavors in these muffins. Thanks for any advice!
Hi Melissa, you certainly can! See “Ingredient Variations/Substitutions” in the post for a few different options. You can replace the applesauce with canned crushed pineapple, swap the orange juice for pineapple juice, or replace the 1 cup of shredded apple with 2/3 cup canned crushed pineapple.
I’m on Weight Watchers and I’m really looking for the nutrition information like fat calories fiber and carbs?
Hi Sherry, 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
Can these be made jumbo sized? If so, how would the cooking instructions change? Thank you!
Hi Lyn, For jumbo muffins, you can follow the baking times and directions from these jumbo blueberry muffins as a guide. Enjoy!
We have an excess of zucchini from our garden. Could well-blotted zucchini be used in place of the carrot or would it be way too much moisture?
Hi Kaili, you can use zucchini here!
Can I make the batter, put it in fridge and make them the next day?
Hi Daphne, 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 bake the muffins right away.
For high altitude (I’m at 7,000 ft): I increased the flour by 2 TB, increased the liquid to 1/2 cup (instead of 1/3), and increased the oil to 1/2 cup (instead of 1/3). I also used golden raisins, no flax seed and added 1 scoop of vanilla protein powder. Turned out extremely moist and rose beautifully! I did not change the baking temps. Thank you for such an amazing recipe- new fave for sure!