Healthy Carrot Zucchini Muffins are naturally sweetened, perfectly moist, and delightfully fluffy. Made from whole grains, naturally sweetened, full of protein from yogurt, and loaded with 2 cups of veggies, these muffins are the perfect healthy breakfast, lunch boxes or a quick snack option.

If you took a peek in my fridge on any given day, I can almost guarantee that you’d find a zucchini and a bag of carrots chilling in my crisper. Both are two of my top veggie staples to keep on hand for easy veggie-loading. I find them so easy to throw into all kinds of dishes, but I especially love both in veggie-loaded muffins.

These Carrot Zucchini Muffins are inspired by my super popular Healthy Lunchbox Muffins. These muffins are equally perfect for lunch boxes, but made with whole wheat flour, plain yogurt, and applesauce for extra soft, fluffy, and moist muffins. Easy to throw together in 10 minutes and baked up to perfection in just 22 minutes, this muffin recipe has 2 cups of veggies in it and is lighter on the sugar than a traditional muffin recipe. It makes 12 perfectly sweetened muffins that store beautifully in your fridge or freezer, so this recipe is perfect to make as part of meal prep. Naturally vegetarian, nut-free and can easily be made dairy-free when you use your favorite plant base yogurt.

Love these muffins? Be sure to check out my Healthy Carrot Oatmeal Muffins and my Hearty Whole Wheat Banana Zucchini Muffins, too!

Do you need to peel the carrots and zucchini for these muffins?

I do recommend peeling carrots before grating. People can sometimes find the skin of carrot bitter and peeling removes that. If you don’t mind the taste of the skin, feel free to leave it on.

Zucchini, on the other hand, has thin, tender, and totally tasty skin. So, peeling is optional and a step I often skip to save time. However, if you have a selective eater in the house that doesn’t love a little green in their baked goods, peeling your zucchini will make it almost melt in these muffins.

How do you squeeze out the carrots and zucchini?

  1. First, peel the carrots and then grate both the carrots and the zucchini.
  2. Then place both in the middle of a paper towel or a clean dish towel.
  3. Wrap up the grated veggies in the towel and press down to draw out the water.
  4. Flip it and press down again. At this point, it should be good to go into the batter for these healthy breakfast muffins.

Tips for baking with whole wheat flour.

First, it is important to know that whole wheat flour is a much “thirstier” flour than APF (all purpose flour). Meaning, it absorbs more liquid. Using APF as a direct swap for whole wheat in a baked good will often result in a wetter (even mushy) bake.

Whole wheat flour is much denser than APF as well. Because of this, it is VERY important NOT to over mix the batter for these carrot zucchini muffins. Mixing activates the gluten in the flour. The more mixing you do, the denser these healthy carrot zucchini muffins will be. For the fluffiest muffins, be sure to mix until JUST combined.

Wondering how to store your carrots so they stay fresh as long as possible? Check out my post on How to Keep Cut Carrots Fresh and get the most out of your produce buck!

Tips and tricks for the best muffins

Let them cool for a bit before enjoying. 

I know nothing is better than warm muffins fresh from the oven. I totally hear ya. But, insider tip, baked goods are still cooking when they are removed from the oven. As they cool, these carrot zucchini muffins will firm up and finish setting. Biting into one of these muffins might make you think they are soggy in the middle and need longer to bake, when actually they are done after cooling!

Don’t over mix the batter. 

On thing that makes these carrot zucchini muffins so great is how fluffy they are. The key to that fluff is to mix the wet and dry ingredients together until JUST combined. Over mixing can lead to dense, flat muffins. Booooo. No one wants that. So stop yourself from over mixing!

How to store these muffins

These muffins can hang out on your counter for a day, but if you plan to enjoy them over several days pop them in the fridge! Keeping them in an airtight container in your refrigerator will help to keep these moist muffins fresh longer and prevent molding.

Or you can freeze them! I like to store them in a large freezer bag or freezer-safe large container. To defrost, I like to take them out of the freezer and leave them on the counter to thaw overnight. Or, you can warm a muffin in the microwave for about 20-30 seconds.

Suggested Adaptations

Add raisins or chocolate chips. Both make these already tasty muffins even better!

Add chopped nuts. Like walnuts or pecans.

Make them dairy-free by replacing the yogurt with your favorite plant-based yogurt or sour cream.

Other veggie-load muffin recipes you will love…

Loving these veggie muffins and are hungry for more?

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A carrot zucchini muffin on a plate with a knife that has been cut in half. There are more muffins and a bowl of milk next to the plate.
4.79 from 23 votes

Fluffy Whole Wheat Carrot Zucchini Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 22 minutes
Cuisine: American
Course: Breakfast
Healthy carrot zucchini muffins are naturally sweetened, perfectly moist, and delightfully fluffy. Made from whole grains, naturally sweetened, full of protein from yogurt, and loaded with 2 cups of veggies, these muffins are the perfect healthy breakfast, lunch boxes or a quick snack option.


  • 1 cup grated zucchini
  • 1 cup grated carrot
  • cups whole wheat flour
  • cup coconut sugar, or granulated sugar
  • teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • 1 teaspoon cinnamon
  • 3 large eggs
  • cup avocado oil, or melted coconut oil or butter
  • 2 teaspoon vanilla extract
  • ½ cup plain yogurt
  • ½ cup unsweetened applesauce, can sub ripe mashed banana


  • Preheat the oven to 375°F and grease or line a 12-cup muffin tin.
  • Place grated zucchini and carrots in the middle of a paper towel or clean dish cloth. Wrap it up and press to remove as much moisture as possible. Set aside.
  • In a large bowl, whisk together flour, coconut sugar, baking powder, baking soda, salt, cinnamon. Set aside.
  • In a medium bowl, whisk the egg, oil, vanilla, yogurt, and applesauce together until combined. Pour the wet ingredients into the bowl with the dry ingredients. Stir until just combined, being careful not to over mix. Batter will be thick.
  • Fold in drained zucchini and carrots. Again, don't over mix.
  • Portion the batter into prepared muffin tins, filling to the top.
  • Bake for 22 minutes or until a toothpick inserted in the middle of a muffin comes out clean.
  • Remove from oven and allow to cool for at least 15 minutes before eating! They will firm up as they cool.
    Allow them to cool completely before storing in fridge in an air-tight container for 5 days or in your freezer for months.
Serving: 1muffin, Calories: 156kcal, Carbohydrates: 18g, Protein: 4g, Fat: 8g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 5g, Trans Fat: 0.01g, Cholesterol: 47mg, Sodium: 190mg, Potassium: 168mg, Fiber: 2g, Sugar: 6g, Vitamin A: 1876IU, Vitamin C: 3mg, Calcium: 69mg, Iron: 1mg