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Healthy Whole Wheat Morning Glory Muffins Recipe

Sarah Pyle



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Start your day right with our Healthy Whole Wheat Morning Glory Muffins recipe! Packed with nutritious ingredients, these muffins are perfect for a wholesome breakfast or snack. And they freeze beautifully for easy meal prep!

close up view of morning glory muffins stacked on white platter

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These Apple Carrot Muffins are my take on Morning Glory Muffins. A quick-bread batter, they mix up really quickly and you can add in any variety of shredded fruits and veggies, dried fruit, and chopped nuts that you want. Sweetened with honey, these muffins are the perfect on-the-go breakfast to keep you full all morning. They are also freezer friendly so perfect for meal prep and make-ahead snacks!

Ingredients for Morning Glory Muffins

Wet Ingredients

  • Applesauce – applesauce keeps the muffins moist so that we don’t have to use as much oil
  • Egg
  • Honey – honey is our sweetener, so no refined sugar here
  • Coconut Oil
  • Vanilla Extract

Dry Ingredients

  • Whole Wheat Flour
  • Baking Soda
  • Salt – Use table salt in baking – if you only have kosher salt, adjust measurement 3/4 teaspoon
  • Ground Cinnamon

Mix-In Ingredients

This is where all the fun begins. Mix and match, substitute or leave out whatever you want:

  • Orange (zest and juice)
  • Shredded Carrot – you can buy these pre-shredded or use a box grater
  • Chopped Pecans
  • Raisins
  • Grated Apple
shredded apple, carrot, chopped pecans, raisins in bowl with muffin batter


  • Large Mixing Bowl
  • Small Mixing Bowl
  • Measuring Cup
  • Measuring Spoons
  • Knife and Cutting Board or Chopper
  • Box Grater or Foot Processor with Grater Blade
  • Microplane
  • Standard 12-cup Muffin Pan
  • Cooking Spray or Muffin Liners
  • 2 ounce Cookie Scoop

How to Make Apple Carrot Muffins

  1. This muffin batter is a quick bread, so the wet ingredients (applesauce, egg, coconut oil, honey, and vanilla extract) go in one bowl. Give it a quick mix to break up the egg and combine.
  2. The dry ingredients (flour, baking soda, salt and cinnamon) go in a separate bowl. Whisk the dry ingredients to combine.
  3. Now, pour the dry ingredients into the wet and stir to combine. At this point, toss in all of your add-ins and stir just to incorporate. Lastly, add the orange juice.
  4. The batter will be very dense because of the sheer volume of stuff mixed in. This is normal. The egg and baking soda will provide plenty of lift when baking to get a fluffy muffin and the applesauce, oil and orange juice keeps the muffins nice and moist.
  5. Portion the muffins using a 2 ounce scoop into baking liners. Bake until a toothpick inserted into the center of the muffin comes out clean. This should take 22-25 minutes.
  6. Allow the muffins to cool completely on a cooling rack. At this point, you can store the muffins in a sealed container for up to 5 days or wrap in parchment and freeze in a freezer bag for up to three months.
morning glory muffin batter portioned in muffin pan

How to Freeze Apple Carrot Muffins

I make a double batch of this recipe at a time to have a good amount in the freezer at all times. My daughter and I can grab them straight from the freezer on our way out the door every morning.

  • To freeze muffins or any baked good, allow them to cool completely. I like to do what is called “Individually Quick Frozen (IQF)” method. To do this, I stick the whole muffin pan in the freezer and freeze the muffins in their muffin liners.
  • Once frozen (this should take 2-4 hours), remove the muffins from the pan and wrap each muffin in a bit of parchment paper or wax paper and place all the muffins in a gallon-size freezer bag. Since the muffins are already frozen before being bagged together, they won’t stick together. You can easily grab one or two muffins as needed.

When you’re ready to eat your muffin, you can either allow it to thaw at room temperature for about 30 minutes or pop it in the microwave for 30 seconds.

baked apple carrot muffins in muffin pan


As I mentioned above, this recipe is perfectly customizable. Feel free to make any of the below substitutions with no change to the baking time. And I can attest that they are equally delicious!

  • In place of coconut oil, feel free to use vegetable oil or melted butter
  • Swap up to half the measurement of whole wheat flour for all-purpose flour
  • Instead of shredded carrot, try zucchini or even sweet potato
  • In place of grated apple, try grated pear or crushed pineapple
  • Swap pecans for your favorite nut and the raisins for any dried fruit

Frequently Asked Questions

How long will these morning glory muffins stay fresh? These apple carrot muffins will keep in an airtight container in the fridge for up to 5 days or frozen for up to 3 months.

Are Morning Glory muffins healthy? It depends on the ingredients used. I made a point to use more healthful ingredients in this recipe so that you can feel good about feeding them to your family and they will keep you full and satisfied longer. By using whole wheat flour, coconut oil and applesauce, we are able to eliminate all butter or vegetable oil and we are using honey instead of refined cane sugar. In a nutshell, I’ve tried to make these as healthy as possible without sacrificing flavor. 🙂

How can I tell when the muffins are done? The easiest way to tell when baked good are baked through is to insert a toothpick into the middle muffin in the pan. If it comes out clean without any batter or crumbs, you’re good to go!

morning glory muffins sitting on white platter

More Baking Recipes

Yield: 18 muffins

Apple Carrot Muffins

morning glory muffins sitting on white platter

Morning Glory muffins are chock full of fruits, vegetables and nuts. They make the perfect portable, freezer-friendly breakfast. Keep a batch in the freezer for a quick, on-the-go snack or breakfast

Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes


  • 1 cup applesauce
  • 1 egg
  • 1/2 cup honey
  • 1/4 cup coconut oil
  • 1 teaspoon vanilla extract
  • 2 cups whole wheat flour
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 Tablespoon cinnamon
  • 1 orange, zested and juiced
  • 1 cup grated carrots (approximately 3 carrots)
  • 1/2 cup pecans, chopped
  • 1/4 cup raisins (soak in hot water for 10 minutes)
  • 1 medium apple, grated


    1. Preheat oven to 350ºF.
    2. In a large bowl, combine the egg, applesauce, honey, coconut oil and vanilla extract. Stir until fully combined. Set aside.
    3. In a small bowl, combine the whole wheat flour, baking soda, salt, cinnamon and nutmeg.
    4. Add the flour mixture to the wet ingredients and stir until just blended.
    5. Add the orange zest, grated carrots, chopped pecans, raisins and grated apple to the batter and stir until well blended.
    6. Add the orange juice and stir to incorporate fully.
    7. Line a muffin pan with paper liners, and then portion 1/4 cup of batter into each liner.
    8. Bake for 22-25 minutes, until a toothpick inserted in the center comes out clean. (If they brown too much on top, cover with aluminum foil to prevent burning.)
    9. Let cool in the muffin pan for 2 minutes.


This muffin is kind of a "kitchen sink" recipe in that so many different ingredients are added. Feel free to swap out or omit any of the fruit, nut and vegetable additions. For example, you can substitute grated zucchini for the grated carrot, you can use crushed pineapple instead of grated apple, mashed banana in place of the applesauce, and you can use any variety of nut or dried fruit. You can even add dried coconut if you like.

Feel free to substitute the one egg in this recipe with a flax egg mixture (1 Tablespoon of ground Flaxseed mixed with 3 Tablespoons of water) and swap the honey for agave nectar if you need to make it vegan.

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Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 150Total Fat: 6gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 10mgSodium: 138mgCarbohydrates: 24gFiber: 3gSugar: 13gProtein: 3g

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By on February 19th, 2024

About Sarah Pyle

Hi, I'm Sarah. The voice behind Feast for a Fraction. I've been a penny-pincher all my life, but still have a taste for nice things. I'm here to show you that you can eat (and live) well on a budget. From recipes and DIY tips to ways to make extra money, we'll be in control of our budgets together!

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20 thoughts on “Healthy Whole Wheat Morning Glory Muffins Recipe”

  1. Such a great recipe! Thank you! We are trying to be gluten free at my house. Do you think gluten free flour would work? Or coconut or almond flour? I would appreciate any guidance!

    • Hi, Kathy! If you have an all-purpose gluten-free baking mix, you could use that in equal measurement. If you want to use only coconut flour, I would try reducing to 1 1/2 cups as coconut flour absorbs a lot more moisture than all-purpose flour. I hope that helps!

    • I can’t have whole wheat flour as I am gluten free, but I am making these with Spelt Flour. Spelt is similar taste and can be used cup for cup instead of whole wheat!

      • That’s very good to know, Selina. Thank you for sharing! I don’t have any experience using spelt flour, but it’s very good to know that it can be used for substitution!

    • Hi, Mary. You could substitute for a gluten-free baking mix, but I have not tested this recipe specifically with oatmeal or oat flour. You could substitute up to 1/4 cup of rolled oats for 1/4 cup of flour without affecting the texture too much.

  2. Hello,
    Thank u 4/sharing ur recipe I’m n/the process of incorporating my dry ingredients but I noticed u said to add nutmeg but in ur list of ingredients u DO NOT mention nutmeg. As a newbie I wld really need the measurements. But since I have already put all the ingredients together, I am going to just maybe put half a teaspoon of nutmeg and hope this works.


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