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 made these…but I made a lot of changes….
    I used garan masala instead of cinnamon – added a nice flavor. I thought I had applesauce, but I didn’t – so I used pumpkin instead and I doubled it because I don’t have an apple… I left out the carrot… but I added dried raspberries and blueberries. I did have flax and whole wheat flour – It looked a little dry so I added a little extra milk (no orange juice). After all that – they are delicious! So great base recipe – very flexible.

    1. These are very good and satisfying. I made your favorite carrot cake for Easter and I haven’t been able to stop eating it. So, I needed a healthier alternative. After baking and eating one of these muffins for breakfast I feel like I’ve done something healthy for myself. Thanks, sally.

  2. Haven’t made these for a while and was CRAVING them….. had all the ingredients, thankfully! I used apple butter instead of applesauce because that is what i had on hand. Added the flax meal, chia seeds and used coconut oil. Ummm Ummm good

  3. one of the bestbakes. Thank u for ur beautiful n never fail recipes time n ever again

  4. Elaine Armstrong says:

    My raisins were old and dried out so I added them to the liquid ingredients and soaked for about 10 minutes to plump them up. Used some mashed banana instead of applesauce. Probably over baked them by a couple of minutes but they were still moist and not dried out at all. I will add these to my muffin rotation.

  5. Lael Dratfield says:

    Would substituting the whole wheat flour with buckwheat flour work?

    1. hi Lael, I have never tried these muffins with buckwheat flour so I’m unsure of the results.

  6. Awesome recipe! These muffins are full of good for you ingredients, but are still moist and delicious and totally hit the spot when you are craving something a little sweet. Followed the recipe exactly and they were perfect.

  7. love this recipe!!! I made the mistake of halving the recipe and had to make another batch the very next day!! I’ve used both apple juice and mango juice, I’ve found that the type of fruit juice doesn’t really make a difference, so you can basically just use whatever you have

  8. I love these muffins!

    It’s great that they have so much fun stuff in them (and that I can pretty much mix and match as I please with what I have in the house). I usually use whole wheat spelt flour (they like spelt in Germany), which makes them a little more dense. I also usually reduce the sugar- sometimes I leave it out entirely and only use the honey as listed in the recipe. Needless to say the recipe is very forgiving, they taste great and have so much good for you stuff in them!

  9. I used all purpose flour but otherwise followed the recipe exactly – I would recommend way more mix-ins that listed!! WAY more raisins/cranberries, nuts, etc. Maybe that’s just my taste. Otherwise, great bake.

  10. Made these this morning. I used pistachios. Oh my! They are so delicious!

  11. This is going to be my go to Morning Glory Muffin recipe! The muffins were so flavorful and moist. I’ve tried several, several recipes and this is the best to date! Love the addition of flax meal. I also like that they are a bit more balanced and on the healthier side.

  12. Absolutely wonderful.
    I used some of your suggested changes but this recipe is a winner including baking temps and times.
    It made 14 for me.
    Thank you.

  13. These were amazing! I made them with all purpose flour and walnuts instead of pecans, and omitted the flax, orange zest and raisins because I didn’t have any. I ended up with 14 muffins. Thank you 🙂

  14. 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!

  15. 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!

    1. 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!

      1. 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!

  16. 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!

    1. I’m thrilled these were such a hit with your family, Carly!

  17. 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

  18. Ashley Zemina says:

    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

  19. Stephanie Westing says:

    These look delicious! Have you ever put zucchini in as well?

  20. Sylvia Doignon says:

    Delicious! and perfect to start the day.

  21. Do you have nutrition info?

    1. Hi Kayla, I’m unsure of the nutritional info of this recipe, but there are many great online calculators like this one:

  22. 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!

  23. 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.

  24. 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.

  25. 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

  26. 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.

  27. Becky Ann Corcoran says:

    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!

    1. 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.

  28. 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!!

  29. 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!

  30. 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.

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