This Pumpkin Zucchini Muffin recipe is flavorful, fluffy, easy to make and the perfect fall baked good! Made with whole wheat flour, grated zucchini, pumpkin puree, applesauce, and a some brown sugar, these moist muffins are a delicious snack or breakfast.

A pumpkin zucchini muffin cut in half on a plate. One half has a little butter on it and there are more muffins on the table next to the plate.

I have been dreaming up this recipe all summer. There is something magical about the fine line that divides seasons. When winter becomes spring. When spring becomes summer. And now, summer tiptoeing into fall. It is just amazing to have the best of both seasons during this small window of transition. The weather is warm during the day and perfectly chill at night for sleeping. And we get to eat pumpkins AND zucchini at the same time.

It is not a flavor combo that many would consider, but it truly is perfection. These Pumpkin Zucchini Muffins are delightfully moist from the grated zucchini and pumpkin puree and full of flavor from spices that compliment both veggies. They are made with whole wheat flour, but are delightfully fluffy. And the combo of applesauce and brown sugar sweeten these breakfast muffins perfectly. Prep takes just 10 minutes and they are done baking in 20. Perfect to make as part of meal prep, since this recipe makes a batch of 12, and they store beautifully in your fridge or freezer.

Bonus: they are dairy-free and nut-free.

So, here is another veggie-loaded muffin recipe to add to your must-bake list!

Tips for baking with whole wheat flour.

People often ask me how I make baked goods fluffy when baking with whole wheat flour (like with these Carrot Zucchini Muffins). And I get ya! Whole wheat flour is full of fiber (yay!), but can make for a much denser baked good than APF (all purpose flour). So, here are some helpful things to know when baking with whole wheat.

Whole wheat flour is a much “thirstier” flour than APF meaning, it soaks up more liquid than other flours. If you are replacing the whole wheat flour with APF in a recipe, know your baked good might be a little moister and you may need to add a touch more flour to get the right consistency.

It is also important to know that 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 Pumpkin Zucchini Muffins.

Mixing activates the gluten in the flour. The more mixing you do, the denser these whole wheat muffins will be. For the fluffiest muffins, be sure to mix until JUST combined.

How do you squeeze out the zucchini for these muffins?

Don’t skip squeezing out the moisture in the zucchini for these muffins! Why? Because it is hard to predict how much water a zucchini holds (a lot of that depends on how large and fresh it is). So, squeezing out the water from zucchini before adding it to the batter for these pumpkin muffins will help ensure that you get to enjoy a perfectly moist muffin that isn’t too wet in the end.

Here is how you do it!

  1. First, grate the zucchini.
  2. Then place 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 and tricks for the best muffins

Let them cool for a bit before enjoying. 

While piping hot muffins fresh from the oven is a special kind of magic, resist the urge to eat these Pumpkin Zucchini Muffins right away. Pump the breaks and let them cool for 10-15 minutes.

Why? Because baked goods are still cooking when they are removed from the oven. As they cool, these 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 they actually don’t.

Don’t over mix the batter. 

I love how fluffy these Pumpkin Zucchini Muffins 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.

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.

Bake as a loaf at the same temperature for about 45-55 minutes.

Use grated carrot instead of zucchini.

Replace the pumpkin with butternut squash puree or sweet potato puree.

Other veggie muffin recipes…

Did you try these veggie muffins and now you’re hungry for more? 

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Pumpkin Zucchini muffins in a basket with a white napkin on a white table.
5 from 11 votes

Fluffy Whole Wheat Pumpkin Zucchini Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Breakfast
These Pumpkin Zucchini Muffins are flavorful, fluffy, easy to make and the perfect fall baked good! Made with whole wheat flour, grated zucchini, pumpkin puree, applesauce, and some brown sugar, these moist muffins are a delicious snack or breakfast.


  • 1 cup grated zucchini
  • 2 cups whole wheat flour
  • teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • 2 teaspoon pumpkin pie spice
  • 1 cup pumpkin puree
  • ½ cup packed brown sugar
  • 2 large eggs
  • ¼ cup avocado oil, or melted coconut oil or butter
  • 2 teaspoon vanilla extract
  • 1 cup applesauce


  • Preheat the oven to 375°F and grease or line a 12-cup muffin tin.
  • Place grated zucchini 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, baking powder, baking soda, salt, and pumpkin pie spice. Set aside.
  • In a medium bowl, whisk the pumpkin puree, egg, oil, vanilla, brown sugar, 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 until just evenly distributed. Again, don't over mix. The secret to fluffy muffins is to mix until ingredients are JUST combined.
  • Portion the batter into prepared muffin tins, filling to the top. Spinkle more brown sugar on top, if desired.
  • Bake for 20-22 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: 175kcal, Carbohydrates: 28g, Protein: 4g, Fat: 6g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.003g, Cholesterol: 31mg, Sodium: 213mg, Potassium: 184mg, Fiber: 3g, Sugar: 12g, Vitamin A: 3252IU, Vitamin C: 3mg, Calcium: 59mg, Iron: 1mg