Morning Glory Muffins

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. My husband and I had just celebrated our 6 month anniversary at a beautiful bed and breakfast in northern Virginia. One morning we were served the absolute BEST muffins. Now, I know the trip was filled with champagne and dessert and all things celebratory, but the muffins truly stuck out to me. They were packed with apples, carrots, brown sugar, pecans, spice, raisins, and more. Basically everything I love in one.

I bake this copycat version all the time and I just updated some of the photos. I also simplified the instructions and added plenty of substitutions so you can play around with the recipe too. 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. 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 mintues
  • 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, 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 muffin sheet, 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


  1. 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!!!

  2. 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!

  3. So good! Baking instructions were on point.

  4. Raena Carson says:

    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.

  5. This recipe is so moist and delicious!

  6. Tie Dye Tina says:

    Excellent! I soaked my raisins in hot water before baking and they were super moist. I used unsweet coconut flakes in place of nuts.

  7. 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.

  8. 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!

  9. 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!!

  10. Beth Hutcheson says:

    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

    1. Absolutely! See step 3. Fill to the top. Here are all of my muffin recipes and most include mini muffin instructions, too!

  11. Mary Poole says:

    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!

  12. 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.

  13. Delicious! This recipe is a keeper – no need to say anything more.

  14. Fantastically delicious! I’m wondering how I could pull off making it as a loaf instead? Is this something anyone has tried?

  15. These are great! Wonderful recipe just as written.

  16. I substituted chia seeds for the flax, because that’s what I had. They are so good. My family loves them.

  17. Absolutely delicious ! I used 1/4 cup of brown sugar and replaced 2 out of the 3 eggs with chia seeds (1 tablespoon chia seeds with 3 tablespoons of water to replace one egg). I baked them at the temperature recommended and they came out high and perfect. This is a recipe keeper ! Thank you !

  18. I have been using the Cooks Country recipe for my Morning Glory muffins but will be using this recipe going forward. It’s a very versatile recipe that can be altered in many ways to meet your desire. I wanted a muffin that would be my pre-workout breakfast with my morning coffee, so I added a large scoop of vanilla protein powder and to give them added moisture, I added one 5oz. Chobani vanilla Greek yogurt and 1/2 cup shredded coconut. To add more fiber I added a 1/2 cup of ground(in blender) high fiber cereal like, Ezekiel Golden Flax. Muffins turned out moist and delicious. What really stood out in the taste was the coconut and mini chocolate chips. One of my best. The other recipe calls for adding pineapple with the juice, but after adding the orange juice, i didn’t miss the pineapple. Very glad I found this recipe.

    Thank you

  19. Made this this week after getting too many carrots in my CSA box. Used pineapple juice instead of the OJ (we had some open) and they were great. Ate some as healthy snacks and we put cream cheese frosting on some and ate as cupcakes after dinner as well.

  20. Can this recipe be made in a bread loaf pan instead of muffin tins?

    1. Definitely! I’m unsure of the best bake time, but use a toothpick to check for doneness.

  21. Absolutely love this recipe. Have passed onto both my daughters. Tried with and without bannana, prefer with. Used MCT liquid coconut oil. Added chopped dried apricots and cranberries. Threw a whole peeled orange into food processor instead of just orange juice. Thanks for this yummy healthy recipe.

  22. I made these muffins for the first time today. I did substitute gluten free flour (Bob’s Red Mill 1 to 1 Baking flour is my usual) and as I read in the comments, I soaked the raisins prior to mixing them in. Muffins came out beautiful, moist, and delicious!

  23. Can I use both ground flax and flax seeds? I already added the flax seeds but I’m wondering if it’s okay for me to add both? Or just stick to the seeds?

    1. Hilari @ Sally's Baking Addiction says:

      Hi Julia, we haven’t tested the recipe with flax seeds in addition to ground flax. For best results, we recommend sticking to the recipe but let us know if you test anything.

  24. These look delicious! Is the orange juice meant to be freshly squeezed or store-bought juice?

    1. Either works!

  25. Fantastic recipe! Easy and delicious! I used dried cranberries and no nuts or orange zest (didn’t have any) but otherwise followed the recipe exactly and they turned out perfect (I managed to get 18 total). I did the nutrition math (for my 18 muffins based on what I used) and for anyone who wants to know, these are only about 150 calories each 🙂 Baked good lovers rejoice!

  26. Just delicious morning pop…not to forget a delight snack! Followed recipe except used whole Chia seed(had no flax)…
    Made 14 muffins and we are ready for another batch!

  27. At first everything turned out great, I made mini muffins. I did not include the flax and instead of apple, I added more carrot.
    After sitting on the counter for an hour they have all turned green. Are these still safe do eat? Any idea why they turned green?

    1. Hi Megan! This is usually a reaction from the baking soda and shredded carrots– give it a quick internet search. It’s normal! And they’re still totally edible.

  28. I tried this recipe and it turned out very nice but the muffins were dry. Any thoughts on this are appreciated! Thank you.

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Tony, Did you make any ingredient substitutions or changes? There are plenty of wet ingredients in this batter as written to keep them moist. Make sure you are measuring your flour correctly (spoon and level, not scoop). Also it’s possible that the muffins were over baked. If you try them again try checking them earlier.

      1. Thanks for the tips! I will try these suggestions.

  29. I’m looking forward to trying this! Could these be adapted to jumbo muffins?

    1. Stephanie @ Sally's Baking Addiction says:

      Sure can, Niki! For jumbo muffins, bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-30 minutes or until the centers are set. Stick a toothpick in the center of a muffin to test for doneness.

  30. Hi! What can I use in place of ground ginger?

    1. Hilari @ Sally's Baking Addiction says:

      Hi Shilpa, you can simply omit the ground ginger, no other changes necessary OR replace the ground ginger with more ground cinnamon. Enjoy!

    2. Alysse Fustaino says:

      this recipe was a win for my picky toddler!! I used zucchini and carrot instead of apple. I omitted 1 egg for 2 bananas, used Greek yogurt instead of the orange juice and coconut sugar instead of the brown sugar. We also added about 1/4 cup chocolate chips and shredded coconut. Delish!!

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