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


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)7. 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. 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

Hands down, one of my favorite muffin recipes! Freezer friendly, wholesome, healthy, and EASY morning glory muffins!
This wholesome muffin has it all! The flavor of these morning glory muffins is incredible and they're super moist.


  1. Love, love, love morning glory muffins. Thank you! This got me wondering. I made your baked oatmeal recipe – a huge hit with my family. Think there is a way to combine the two recipes – the flavors of morning glory muffins with baked oatmeal? Hmmm…

    1. Hi Jen! You can leave out the berries in the baked oatmeal and add shredded carrots and apples, along with some ground ginger (there’s cinnamon already there!) and raisins (and/or pecans), too. Delicious. Enjoy!

    2. Okay…let me say these are our favorite muffins!! Love how there are so many yummy textures going on! Thank you for this yummy recipe! I add flax seed, hemp, and chia seeds for that extra healthy kick!

  2. These are delicious! I made them with dried cranberries instead of raisins and omitted the ground flax (just because I didn’t have any). The whole family loved them, including my 5 year old and 16 month old. I used an online recipe calorie counter, and with the modifications (cranberries instead of raisins and no ground flax seed), for a yield of 16 muffins, it came out to 218 calories per muffin, which is great!

  3. I made these today, and have a question: I found with 2 tsp baking soda in them, there was a lingering taste from that which I didn’t prefer… I’m wondering if you know of any reason these wouldn’t work as well with both baking soda and baking powder, to lessen that soda-y taste. They’re a fairly involved recipe, so when I make them again, I want them to turn out well. I don’t want to sub in baking powder if there’s good reason to stick with the full amount of soda. What are your thoughts?

    1. Hi Margo! You can definitely play around with this recipe and use some baking powder to replace the baking soda. Just remember that baking soda is 4x stronger than baking powder. And depending how much you replace– I fear with that much extra baking powder, the bitter aftertaste would be quite pungent.

    1. Hi Michele, Whole wheat pastry flour is lighter in texture and lower in both protein and gluten. I have not tested it so I’m unsure if pastry flour would hold up to the moisture in this batter. If you try it out please let me know!

      1. I used whole wheat pastry flour today and they turned out perfect! I also used it in place of whole wheat flour in your banana bread. I use it in most of my quick bread/muffin recipes – all good! I made your red velvet cake for my twins late birthday celebration yesterday. While I didn’t use enough food colouring to get that beautiful red shade, everyone loved it!

  4. I have small children, so we often make mini muffins. How would I change the cooking temperature/time to accommodate mini muffins? These were delicious!

    1. Hi Courtney, For mini muffins, bake for 11-13 minutes at 350°F (177°C) the entire time or until a toothpick inserted in the center comes out clean.

  5. These are so good! Well worth the tiny bit of extra effort to prepare the ingredients. They even got the thumbs up from my 6- and 4-year-olds. And don’t leave out the orange zest/juice if you can help it – such a great background flavor! Thank you for this recipe!

  6. These are amazing! The flavor of a carrot cake, but no guilt! I only had one full-sized muffin tin, so I did the rest of the batter in a mini muffin tin (425F for 5 minutes, 350F for 12 minutes and they tested done, yielded 12 additional mini muffins). I’m not a huge fan of the flavors of whole wheat flour or flax seed, but I can’t detect them at all in the finished product. These will be a great grab-and-go breakfast!

  7. These are amazing! I was looking for a muffin with some fiber for my 3 year old son who has tummy troubles and this is it! I substituted prune puree for the applesauce and they are still delicious. Very light/soft crumb with just the right amount of sweetness. Thank you!

    1. Hi Susanne, I’m unsure– this would require additional recipe testing. You could try replacing the ground flax with it. Let me know if you try anything!

  8. After mixing the batter for these I realized I somehow misplaced my muffin pan. To sub I made these in a 8×8 pan and cooked at 350 the whole time and they turned out fantastic! Great texture and flavor. Thanks for another knockout

  9. Made these this weekend. I was able to stretch the recipe to 24 muffins. My only complaint is the lack of coconut in the recipe (but honestly that’s kind of on me for forgetting that I was going to put it in). I added less honey and more applesauce than recommended and I definitely see why more honey would be better. Regardless, this is a great recipe and it’s definitely my new go-to for morning glory muffins.

  10. I adjusted a batch for my toddler, omitted the sugar and honey and subbed some chopped dates soaked in water (added enough date liquid to make up for the missing honey).

    Both batches were delicious!

    Little guy just ate 3 of his. Big hit!

  11. Awesome recipe! Thank you Sally! My muffins came out moist and tender and they rose beautifully even with substitutions ( I subbed the whole wheat for spelt and omitted the brown sugar and replaced it 1/4 cup of lucuma powder and pure stevia ). You are a baking rockstar, all of the recipes I have tried from your site have been successful which does not happen often with recipes I try from blogs.

1 4 5 6

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

With kitchen-tested quality recipes and step-by-step tutorials, my goal is to give you the confidence to bake and cook from scratch.

Recipes You’ll Love



Sally's Baking Challenge

Join the community on the 1st of every month as we tackle a new challenge recipe.

View More

Sally's Cookie Palooza

A tradition since 2013, every December we countdown to Christmas with 10 new cookie recipes in a row!

View More

Sally's Pie Week

The first week of every November is all about Thanksgiving Pies.

View More

My Cookbooks

About Sally

Welcome to my Kitchen!

I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally