Morning Glory Muffins with Fresh Milled Flour: Easy Whole Wheat
Morning Glory Muffins are more than just shredded veggies. They are a delicious, healthy carrot zucchini muffin that tastes like carrot cake but packs the nutritional benefit of whole grains. This easy recipe is a great way to start the day and makes the best on-the-go snack!

This healthy morning glory muffin recipe with whole wheat, carrots, and zucchini is a staple in our household. It’s easy, delicious, and is a great way to use up extra veggies. It is a very forgiving recipe that uses white whole wheat flour for the perfect texture and added nutrition.
Zucchini carrot muffins are one of those easy bakes that sound like a great way to get in extra veggies. And it can be! We just want to balance those healthy vegetables with lots of delicious flavor and the right amount of natural sweetness so the end result is irresistible.
We love these as a breakfast side with sausage balls (no Bisquick required!) or a protein-rich breakfast casserole. They are also a great snack with greek yogurt or with a dollop of peanut butter. Try these healthy carroty zucchini muffins the next time you want a nutritious snack or breakfast option.
If you’re wanting to bake more with fresh milled flour, muffins and quick breads are a great place to start! Try whole wheat blueberry muffins, fresh milled zucchini bread, fresh milled flour biscuits, or fresh milled English muffins for delicious and nutritious options! We also love freshly milled sandwich bread and freshly milled sourdough bread.

Why You’ll Love This Recipe
Simple ingredients, great flavor: I am always looking for healthy recipes for our family, and this one fits the bill. Zucchini carrot muffins use simple, pantry staple ingredients and pack a delicious punch as well.
Added nutrition: Using freshly milled whole wheat flour adds both protein and fiber to this recipe, not to mention all of the vitamins and minerals that all purpose flour just does not contain. Freshly ground flour has almost 16 grams of protein and 13 grams of fiber per cup. This is more that your regular whole wheat flour!
Great for meal prep: I usually make a big batch of these and freeze them. Simple store in a sealed container or freezer bag. When you want to eat them, either take some out and place in the fridge for the week or let them sit at room temp before toasting.
What are Morning Glory Muffins/Whole Wheat Carrot Zucchini Muffins?
Whole wheat carrot zucchini muffins are a delicious quick bread type recipe that uses whole wheat flour and shredded vegetables. This combination has lots of nutrients and is considered healthier than other muffins. Using freshly milled flour adds even more vitamins, minerals, and protein as the flour contains both the bran and the germ. This is considered superior when it comes to nutrition, but this recipe can definitely be made with store-bough whole wheat flour.

Morning Glory Muffins (Whole Wheat Carrot Zucchini Muffins) Ingredients
Freshly milled soft white wheat berries: Milling flour just before baking is the best way to preserve all the vitamins, minerals, and nutrients that flour contains. It makes the best, hearty muffins! You can use whole wheat pastry flour or store-bough whole wheat flour as well. If you use all-purpose flour, make sure to place your shredded zucchini in a paper towel and squeeze out the excess moisture.
Applesauce: Applesauce gives this recipe a bit more flavor and helps lock in moisture. You can substitute the same amount of mashed banana if you don’t have apple sauce.
Neutral oil: I like to use avocado or coconut oil. You could use vegetable oil, but it is usually highly processed.
How to Make Morning Glory Muffins (Whole Wheat Carrot Zucchini Muffins)
- Preheat your oven to 350 degrees and mill your flour. To get 1 & 3/4 cup flour, use about 1 1/4 cup soft white wheat berries. Line a muffin tin with 12 muffin cups or grease the inside of the pan to prevent sticking.
- Shred and measure out zucchini and carrots.
- In a large bowl or in the bowl of a stand mixer, combine the wet ingredients: shredded zucchini, shredded carrots, applesauce, maple syrup, eggs, avocado oil and vanilla extract until well combined. Set aside
- In a separate bowl, combine the dry ingredients: fresh milled flour, baking soda, cinnamon, and salt.
- Add the dry ingredients to the wet ingredients and mix until just combined. Do not over-mix. Fold in any add-ins that you like.
- Use an an ice cream scoop or spoon to transfer the batter into the center of a muffin cup.
- Bake for 20-25 minutes or until a tester comes out clean.
- Allow muffins to cool in the pan for 5-10 minutes, then remove and transfer to a wire rack to finish cooling.


Recipe Tips
- You do not need to remove the excess liquid from the zucchini when baking with freshly milled whole grain flour. The flour will soak up the extra liquid, and the muffins will come out moist and delicious.
- You can substitute 3/4 cup of the fresh milled flour with oat flour. To make oat flour, add whole oats to a food processor and pulse until a fine powder forms. Oat brans can add extra taste and texture.
- Make a double batch easily. Store in an airtight container at room temp for up to 2 days, then refrigerate. These muffins also freeze really well.
- We love to make these as mini muffins! These are such an easy snack before breakfast or when we’re on the go.
Morning Glory Muffins/Whole Wheat Carrot Zucchini Muffins Variations
You can add any of your favorite dried fruits and nuts to this recipe! Add up to 1 cup of add-ins to mix it these whole wheat muffins and make it different. Popular add-ins include:
- Raisins, golden raisins, cranberries
- Shredded coconut
- Chocolate chips
- Chopped pecans, walnuts, almonds
Try the recipe as-is the first time, then add some nuts and chocolate chips the next time!

Recipe FAQs
I hope you enjoy this recipe as much as we do!
Morning Glory Muffins with Fresh Milled Flour
Morning glory muffins are more than just shredded veggies. They are a delicious, healthy muffin recipe that tastes like carrot cake but packs the nutritional benefit of whole grains.
Ingredients
Wet ingredients
- 1 cup shredded zucchini (about 1 medium zucchini)
- 1 cup shredded carrots (about 2 medium carrots)
- ⅓ cup unsweetened applesauce
- 1/2 cup pure maple syrup
- 2 eggs
- 1/3 cup neutral oil
- 1 teaspoon vanilla extract
Dry ingredients
- 1 & 3/4 cup fresh milled flour from soft white wheat berries
- 1 teaspoon baking soda
- 1 & 1/2 teaspoons cinnamon
- ¼ teaspoon salt
Optional add-ins
- ⅓ cup each raisins, cranberries, shredded coconut, chocolate chips, or chopped nuts of choice (up to 1 cup add-ins)
Instructions
- Preheat your oven to 350 degrees and mill your flour. To get 1 & 3/4 cup flour, use about 1 1/4 cup soft white wheat berries. Line a muffin pan with 12 paper liners or grease the inside of the pan to prevent sticking.
- Shred and measure out zucchini and carrots.
- In a large mixing bowl or in the bowl of a stand mixer, combine the wet ingredients: shredded zucchini, shredded carrots, applesauce, maple syrup, eggs, avocado oil and vanilla extract until well combined. Set aside.
- In a separate small bowl, combine the dry ingredients: fresh milled flour, baking soda, cinnamon, and salt.
- Add the dry ingredients to the wet ingredients and mix until just combined. Do not over-mix. Fold in any add-ins that you like.
- Use an an ice cream scoop or spoon to transfer the batter into the prepared muffin cups.
- Bake for 20-25 minutes or until a tester comes out clean.
- Allow muffins to cool in the pan for 5-10 minutes, then remove and transfer to a wire rack to finish cooling to room temperature.
Notes
- You do not need to remove the excess liquid from the zucchini when baking with freshly milled whole grain flour. The flour will soak up the extra liquid, and the muffins will come out moist and delicious.
- You can substitute 3/4 cup of the fresh milled flour with oat flour. To make oat flour, add whole oats to a food processor and pulse until a fine powder forms. Oat brans can add extra taste and texture.
- Make a double batch easily. These muffins freeze really well.
- We love to make these as mini muffins! These are such an easy snack before breakfast or when we're on the go.
Recommended Products
As an Amazon Associate and member of other affiliate programs, I earn from qualifying purchases.