Healthy Zucchini Muffins with Fresh Milled Flour

Last Updated on May 30, 2026 by Kimberly

The inspiration for these healthy zucchini muffins comes from our garden. We have raised a small garden for the past three years. In Florida, you can garden all year long! Our soil is very sandy and does not have a lot of nutrients. The last two years we have added a lot of compost and garden soil. This year, our zucchini plants are huge!

Why You’ll Love Healthy Zucchini Muffins

Zucchini is full of vitamins, minerals, antioxidants, and fiber. It’s especially high in vitamin C and beta-carotene which support eye health.

To use up our zucchini, we make a lot of muffins. Zucchini makes muffins moist and flavorful. Making muffins is a great way to get your kids to eat extra veggies!

How to Process Garden Zucchini

After picking, I wash the zucchini, slice it up, scoop out the seeds, throw the slices in the Ninja Food Processor, and push the chop button. If the zucchini skin is tough, I will peel it first.

When you harvest zucchini early, you can leave the small seeds in. Since the zucchini is chopped fine, you can also put it in spaghetti sauce without anyone noticing.

While processing zucchini, I chop up a few at a time, put the diced-up zucchini in a kitchen towel, and squeeze out as much water as I can.

I will place whatever I am not using that day in a plastic freezer bag and freeze it laying flat. After gardening season is over, I still have zucchini in the freezer, chopped up and ready to go.

Ingredients for Healthy Zucchini Muffins

To make zucchini muffins, preheat your oven to 350°F and gather your ingredients. You will need:

• ½ cup olive oil
• 2 cups of sugar
• 3 eggs
• 1/2 cup sour cream (or plain yogurt)
• 1 teaspoon vanilla
• 3 ¾ cups of fresh milled wheat flour from soft white wheat berries (can substitute 3 cups organic all-purpose flour)
• 1 teaspoon baking soda
• 1 teaspoon salt
• ½ teaspoon cinnamon
• ¼ teaspoon baking powder
• 1 scoop unflavored protein powder (optional)
• 2 cups shredded zucchini
• 1 cup chocolate chips

How to Make Healthy Zucchini Muffins

Cream your oil and sugar together, then add eggs, sour cream (or plain whole milk greek yogurt), and vanilla.

Stir the flour, baking soda, salt, cinnamon, baking powder, and protein powder (optional) together in a separate bowl. Gradually mix into the wet ingredients.

Fold in 2 cups of zucchini and 1 cup of chocolate chips. Zucchini and chocolate pair perfectly together!

Baking Healthy Zucchini Muffins

Place muffin liners in your muffin tins. I like these unbleached muffin liners on Amazon. Spoon the batter in until the muffin cups are 2/3 of the way full and bake at 350°F for 20 minutes.

Healthy Zucchini Muffins with Fresh Milled Flour

Healthy zucchini muffins made with fresh milled flour—soft, moist, and easy to make for a wholesome snack or breakfast.

Print Recipe Pin Recipe

Prep Time 30 minutes mins

Cook Time 20 minutes mins

Total Time 1 hour hr 10 minutes mins

Course Breakfast

Servings 24

Ingredients

  

• 1/2 cup olive oil
• 2 cups organic cane sugar
• 3 eggs
• 1/2 cup sour cream (or plain whole milk greek yogurt)
• 1 tsp vanilla
• 3 3/4 cups fresh milled wheat flour
• 1 tsp. baking soda
• 1 tsp. salt
• 1/2 tsp. cinnamon
• 1/4 tsp. aluminum-free baking powder
• 2 cups zucchini, grated
• 1 cup chocolate chips
• 1 scoop unflavored protein powder optional

Instructions

 

• Preheat your oven to 350° F. Cream the olive oil and sugar together. Add eggs, sour cream (or yogurt), and vanilla. Mix thoroughly.
• In a separate bowl, combine the fresh milled wheat flour, baking soda, salt, cinnamon, baking powder, and protein powder (optional). Add to wet ingredients and mix.
• Fold in grated zucchini and chocolate chips.
• Line muffin pan with liners. Fill 2/3 of the way full with batter. Bake at 350° F for 20 minutes. Let pan cool on baking rack.
• If you make this recipe, please scroll to the comments and give it a rating. This helps my website so much!
Adding unflavored protein powder to these muffins is a great way to boost the protein in your kids' diet!

Notes

This recipe makes 2 dozen muffins.

How to Store and Reheat Healthy Zucchini Muffins

To store short term – If using right away, leave muffins in an airtight container on the counter. Refrigerating baked goods will make them dry.

To store long term – Often, I will double the recipe, pop the muffins in a freezer bag when cool, and stick them in the freezer for a quick weekday breakfast.

To reheat – I will pull the muffins from the freezer and let them thaw overnight on the counter.

FAQs

Can I use frozen zucchini for this recipe?

Yes, you can. If using frozen zucchini, you will find there is plenty of water left in the freezer bag when it thaws. Drain some of the water, but leave some to pour in with the zucchini.

Can I substitute all-purpose flour for this recipe?

Yes, I recommend organic all-purpose flour to reduce glyphosate exposure. If you substitute, only use 3 cups of all-purpose flour.

Can I make healthy zucchini muffins ahead of time?

Yes, they taste great the day after. If making more than a day in advance, I recommend freezing them.