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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 available so you can truly make them your own.

morning glory muffins

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
  • 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!

morning glory muffins

morning glory muffins

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 healthful 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. 🙂

morning glory muffins ingredients and batter

morning glory muffin batter in muffin pan

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, 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.

healthy morning glory muffins

morning glory muffins

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 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!

healthy morning glory muffins

More Healthful Baked Goods

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Morning Glory Muffins

Morning Glory Muffins

  • Author: Sally
  • Prep Time: 30 minutes
  • Cook Time: 24 minutes
  • Total Time: 1 hour
  • Yield: 1416 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


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.


  • 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 flax (optional)
  • 3 large eggs
  • 1/2 cup (100g) packed light or dark brown sugar
  • 1/4 cup (85g) honey
  • 1/3 cup (80ml) vegetable, 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


  1. 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.
  2. 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 just until combined and no pockets of flour remain.
  3. Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425 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. (For mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.) Allow the muffins to cool for 10 minutes in the pan, then transfer to a wire rack to cool until ready to eat.
  4. Cover leftover muffins and store at room temperature for 2 days or in the refrigerator for 1 week.


  1. 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.
  2. Substitutions: See blog post above for all substitutions I’ve tested.
  3. 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.
  4. 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 Questions and Reviews

  1. Made these with our garden zucchini in place of carrots and maple syrup instead of honey and they were perfect!  I love having my recipes from your site always turn out just like they should!  This recipe is a keeper.

  2. These are delicious, and this recipe will replace my current one. They came out very moist and cake-like. I used all whole wheat flower and pumpkin seeds instead of the pecans. Next time, I will leave out the honey and replace it with a ripe, mashed banana. They were not overly sweet, but reducing sugar more will not hurt these. Thanks for the recipe!

  3. I just made these, used whole wheat flour, agave nectar, 2/3 cup coconut oil, 1/2 cup dried cranberries, 1 cup shredded carrots, 1 cup shredded zucchini, applesauce, half an apple grated, 1/2 cup dried sunflower seeds (goodies), just sensational.  Otherwise followed the recipe exactly.  Many different flavors blending together.  Highly recommend this recipe!  Very versatile.  

  4. Made these this weekend. The muffins are really yummy and the recipe seems pretty forgiving! I made them as written, but suspect the batter would be easily customized. The muffins are really moist, but not in the gummy or tacky way muffins can be sometimes. Thank you Sally! 🙂

  5. I made these muffins last night- amazing recipe! Just what I was looking for, something that I could throw a bunch of healthy things into and would still be delicious. I followed the recipe exactly. My only note, and if its even possible, I found them too moist and so I’d put in much less oil next time. 

  6. These muffins were a huge hit. My 11 year old son is so picky, but he loved them. I tweeked things a little, i did 1 cup of flour and 1 cup of oats. Added chia seeds and flax. My daughter, 9, not as picky as her brother, lite up like a Christmas tree when she realized there was chocolate chips inside. Very happy with these and will be making again. I actually got 24 muffins out of this receipt. Thank you for sharing this! 

  7. These are fabulous! The only alterations I made was adding chopped dried apricots instead of raisins (was out) , but threw. In some cranberries as well ! Delicious! Yea for cream cheese frosting too! Thanks Sally , love your recipes!

  8. What a wonderful recipe! I’ve just made these little guys with additional banana and chia and they turned out light and fluffy and smell divine! Thank you for another great recipe Sally. This is the third recipe l’ve followed from you and your measurements, baking temperatures and baking times are always accurate. Thank you for your reliability and attention to details. Greetings from Cologne, Germany

  9. I made these and swapped greek yogurt for applesauce and made them in mini muffin tins. They turned out awesome! I also tend to cut back on sugar and did cut back a little, but I would say that the recipe has just the right amount of sugar and I didnt need to cut back at all. I want to try making the tropical version of these sometime, the idea sounds really good. Thanks for such a delicious recipe!

  10. I just made these and they’re amazing! I used maple syrup instead of honey and really ripe mashed banana and they are fluffy and delicious. Thanks so much! I love your recipes!

  11. Can I leave out the ground flax or substitute something else for it like bran or do I need more flour?

  12. These muffins are so delicious. They are moist, hearty, full of flavor, I could go on and on. These are perfect for a on the go breakfast. These also have really healthy ingredients which I like:)

  13. I just made these and they are delicious! I left out the flax and nuts and probably should have bumped up the raisins because I love them in baked goods. Amazing rise on these muffins they look like they’re from a bakery! Just sweet enough and super flavorful!

  14. SO thrilled to find this recipe. I adapted it to make it gluten free and they are by far my favorite muffins. Thank you.

  15. Amazing! I used sweet potato instead of carrots, walnuts, maple syrup instead of honey and coconut oil. Packed full of goodness! My daughter won’t even know she’s eating veggies!

  16. I”m obsessed with these muffins!! I made them yesterday and can’t stop eating them. How could you adapt this recipe for a 2 or 3 layer cake with cream cheese frosting? This would be a great fall cake. Thanks Sally!

  17. This recipe is awesome! I wanted to take some to work with me for my coworkers and decided a loaf or ring would be easier to transport. Turns out with a little extra time in the oven the batter makes a very pretty bundt cake, too!

  18. I just made these using oat flour as a substitute because I am gluten free and I have been using oat flour a lot recently. (GF oat flour crepes! Yum!). They came out perfectly done using the rest of your recipe exactly. It made 12 muffins and a small loaf pan filled 1/4 of the way.
    I only recently found your site and I am so happy I did!
    Thank you!
    Ps: if you ever need a gf recipe tester, let me know. I’d love to do it!

  19. Love this recipe. Things I did different: I used half plain flour half wholemeal flour, left out the flax seed (didn’t have any) and used sultanas instead of raisins. They’re so hearty, just like a muffin should be. I find the ‘modern’ muffin to be too much like an oversized cupcake.
    This weekend I plan on making at least a double batch of the base mix and then dividing the mix to make some different flavours like I used to when I made muffins at a bakery. I’ll also make a gluten free version for my friends kid and sneak in some zucchini.

    1. Oh, and it made 12 muffins for me, baked directly in the muffin tin with no liners. I think the muffin tins we have in Aus may be a little bigger than yours in the US? Or I just overfilled slightly but they turned out just fine and within the cooking time stated too.

  20. Just finished making these and I could barely wait for them to cool. They are heavenly! I’m gluten free and I just replaced the wheat flour with gluten-free AP flour and I couldn’t tell a difference! Thanks for the great recipe, once again!

  21. These came out so good! I put carrots, zucchini, apples and a little bit of vanilla yogurt in. My kids loved them. Even my picky 1 year old. Your recipes never fail me. Thank you for your recipes.

  22. These muffins are the bomb! Loved everything about them. Could equal amounts of chopped prunes or dates be used in place of the raisins? Thank you for sharing!

  23. I love these muffins. I make them time and time again. I love all the substitutions and extra add in options you’ve listed. Thanks so much!

  24. I just made these banana muffins, I added just a little bit of chopped pecans and made 6 jumbo muffins. WELL, these muffins are absolutely DELICIOUS!!! Not too sweet and so moist that you dont even need to drink anything with it to enjoy them but they are still great with coffee or a glass of cold milk. I will definitely be making these again but I will double the recipe seeing my daughter has already eaten 2 of them . Thank you for this amazing recipe!

  25. Didn’t have time or patience to grate apples, just diced them up. It added a wonderful texture, will continue to dice them instead of grating. Also added a bit of shredded coconut, just because. Absolutely my best batch ever, and I’ve made A LOT of batches!

  26. I never leave ratings but this recipe is so amazing I felt compelled to do so. Great balance, not too sweet, not full of oil/butter but still super moist, tons of flavor. Used coconut oil and threw in the shredded coconut as suggested. LOVE. Thank you, Sally!

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