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. and vanilla extract. The orange zest and ground flax are totally optional, but I usually add both for extra flavor.
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 (dairy or nondairy) 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!

More Healthful Baked Goods
Whole Wheat Banana Bread
Breakfast Cookies
Chocolate Zucchini Bread
Baked Oatmeal Cups
Chocolate Banana Muffins
Bran Muffins
Vanilla Almond Granola or Pumpkin Granola

4.9 from 203 reviews
Morning Glory Muffins
Author:Sally
Prep Time:30 minutes
Cook Time:24 minutes
Total Time:1 hour
Yield:14–16 muffins
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Description
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.
Ingredients
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 flaxseed (optional)
3 large eggs, at room temperature
1/2 cup (100g) packed light or dark brown sugar
1/4 cup (85g) honey
1/3 cup (80ml) vegetable oil, 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
Instructions
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.
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 until just combined and no pockets of flour remain.
Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425°F; 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 pan, then transfer to a wire rack to cool until ready to eat.