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These Healthy Pumpkin Zucchini Muffins are a nutritious fall snack, made with whole grains and naturally sweetened. Some optional mini chocolate chips make them extra yummy!

One half of a Healthy Pumpkin zucchini muffin stacked on top of a whole pumpkin zucchini muffin.

We’ve been making these pumpkin zucchini muffins on repeat. My 3 year old shouted “Hurray!” when I said we would be eating pumpkin zucchini muffins for snack last week. Will he eat zucchini any other time? No. But in this muffin, he is a fan. It might be the chocolate chips?

Ingredients for Healthy Pumpkin Zucchini Muffins. Maple syrup, melted butter, pumpkin puree, eggs, whole wheat pastry flour, zucchini, mini chocolate chips, baking powder, cinnamon, pumpkin spice, plain Greek yogurt, milk, vanilla extract, salt, baking soda.

You all know the drill by now – we are a muffin family – I have quite a few healthy muffin recipes on this site, the most popular being these Peanut Butter Banana Muffins followed closely by these Pumpkin Banana Muffins. A few years ago, someone asked me to develop a Pumpkin Zucchini muffin and it took awhile but I finally did it!

Pumpkin Zucchini Muffin batter

How to make muffins that are fluffy, not tough and dense

There is a secret to making muffins that are fluffy instead of dense and tough โ€“ itโ€™s called the muffin method and itโ€™s important! The muffin method is just mixing the dry ingredients, mixing the wet ingredients in a separate bowl, and then pouring the wet ingredients into the dry ingredients. Stir the wet and dry ingredients until just mixed. It is very important not to over mix here. Overmixing produces more gluten, which is what gives you tough and dry muffins.

Pumpkin Zucchini Muffin Batter in a muffin tin, topped with chocolate chips.

Ingredients for Healthy Pumpkin Zucchini Muffins

  • Pumpkin Puree – I use canned pumpkin puree. Be sure you are using pure pumpkin and not pumpkin pie filling.
  • Grated Zucchini – I don’t peel my zucchini because I like the flecks of green, but you can peel it if you want. Measure the zucchini after grating and then squeeze out the moisture before adding to the batter.
  • Plain Greek Yogurt – Adds moisture and helps make the muffins fluffy.
  • Melted Butter – just a quarter cup. I prefer using butter to oil as it gives a richer flavor. You can use vegan butter if you prefer.
  • Pure Maple Syrup – adds a touch of natural sweetness
  • Milk and eggs – adds moisture and structure.
  • Whole Wheat Pastry Flour – I use this or white wheat flour interchangeably for a lighter texture to the muffins with all the benefits of whole grains that you get from whole wheat flour. Note: King Arthur is now calling their white wheat flour “golden wheat flour” but it is the same product.
  • Baking powder and baking soda – no, they are not the same thing and yes, you need both! These are what makes the muffins rise up and get nice and fluffy.
  • Spices and flavors – Cinnamon, pumpkin pie spice and vanilla extract. See my recipe for homemade pumpkin pie spice HERE.
  • Salt โ€“ donโ€™t skip it! Without salt, these muffins will be bland.
  • Mini chocolate chips – optional, I GUESS??? Regular sized chocolate chips will work here as well.
Pumpkin zucchini muffins topped with mini chocolate chips.

Tips for making the best Pumpkin Zucchini Muffins

  • The most important tip that I can never say enough is DON’T OVERMIX YOUR BATTER. This is why we first mix the dry ingredients really well, then mix the wet ingredients really well, then add them together and carefully mix until just combined and you don’t see any dry spots of flour anymore.
  • Start with a hotter temperature, then reduce after 5 minutes – we start at 425 degrees F and then after baking for just five minutes, then keeping the muffins in the oven, reduce the heat to 350 F. The initial blast of heat activates the baking powder and will help the muffins rise higher.
  • Measure your zucchini before squeezing out the moisture. After you measure out one cup, use a clean towel (or paper towels) to squeeze out as much excess moisture from the zucchini as possible. This will help keep your muffins from getting gummy.
  • Don’t use paper liners – only use parchment liners, or spray the muffin tins liberally with cooking spray and use no liners. I swear by THESE parchment paper liners.

How to freeze muffins

These muffins freeze beautifully. Allow the muffins to cool completely on a rack before freezing. Then they can be individually wrapped in plastic wrap if you like and stored in a freezer bag. They will keep for up to one month.

healthy pumpkin zucchini muffin on a cooling rack.

Helpful equipment for making pumpkin zucchini muffins

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Healthy Pumpkin Zucchini Muffins

Prep 10 minutes
Cook 22 minutes
Servings 12 Muffins

Ingredients 

  • ยผ cup butter melted
  • 1/2 cup greek yogurt
  • 1/2 cup maple syrup
  • 1/4 cup milk
  • 3/4 cup pumpkin puree
  • 1 cup grated zucchini squeeze to remove excess water
  • 2 eggs
  • 1 teaspoon vanilla extract

Dry ingredients

  • 1 and 3/4 cups whole wheat pastry flour
  • 1 tsp pumpkin spice
  • 1 tsp cinnamon
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1/2 teaspoon fine sea salt

Add ins

  • 1 cup mini chocolate chips optional. Reserve about 1/4 cup to sprinkle on top before baking. Regular sized chocolate chips will also work.

Instructions 

  • Move oven rack to the center of the oven, preheat oven to 425 degrees F. Prepare a 12-well muffin tin by either spraying with cooking spray OR lining with parchment paper muffin liners (do not use regular liners, they will stick).
  • In one bowl, combine the WET ingredients, mixing well.
  • In a second bowl, combine the DRY ingredients, mixing well.
  • Add the wet ingredients to the dry ingredients. Use a spatula to mix the two together just until no dry spots of flour are visible. DO NOT over mix. Do not use an electric mixer, this is best done by hand.
  • Add mini chocolate chips and stir one or two times until just mixed in. Reserve about 1/4 cup of the chocolate chips to sprinkle on top of the muffins before baking.
  • Portion out the batter evenly between the 12 muffin wells. I use an ice cream scoop to make this easy. Sprinkle a few chocolate chips on top of each muffin.
  • Place muffin tin in the center rack in the oven, set timer for 5 minutes. After 5 minutes of baking at 425 degrees F, reduce the heat to 350 degrees F and set a timer for 17 minutes. Keep the muffins in the oven when you do this, do not remove them or open the oven door.
  • Bake for the additional 17 minutes, and up to 22 minutes. Check to see if muffins are done by inserting a toothpick into the center of a muffin. If it comes out clean, they are done. Remove from oven and as soon as cool enough to handle remove the muffins from the muffin tin and place on a cooling rack to finish cooling.
  • Muffins can be kept at room temperature in an airtight container for about 2 days or frozen for up to 3 months. See freezing instructions below.

Notes

    • The most important tip that I can never say enough is DON’T OVERMIX YOUR BATTER. This is why we first mix the dry ingredients really well, then mix the wet ingredients really well, then add them together and carefully mix until just combined and you don’t see any dry spots of flour anymore.
    • Start with a hotter temperature, then reduce after 5 minutes – we start at 425 degrees F and then after baking for just five minutes, then keeping the muffins in the oven, reduce the heat to 350 F. The initial blast of heat activates the baking powder and will help the muffins rise higher. Don’t forget to turn down the heat after 5 minutes or the muffins will burn.
    • Measure your zucchini before squeezing out the moisture. After you measure out one cup, use a clean towel (or paper towels) to squeeze out as much excess moisture from the zucchini as possible. This will help keep your muffins from getting gummy.
    • Don’t use paper liners – only use parchment liners, or spray the muffin tins liberally with cooking spray and use no liners. I swear by THESE parchment paper liners.
  • ย 
    • These muffins freeze beautifully. Allow the muffins to cool completely on a rack before freezing. Then they can be individually wrapped in plastic wrap if you like and stored in a freezer bag. They will keep for up to three months if properly stored.

Nutrition

Serving: 1muffin | Calories: 233kcal | Carbohydrates: 35g | Protein: 5g | Fat: 9g | Saturated Fat: 5g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 0.2g | Cholesterol: 41mg | Sodium: 248mg | Potassium: 219mg | Fiber: 3g | Sugar: 19g | Vitamin A: 2606IU | Vitamin C: 3mg | Calcium: 82mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast, Snacks
Cuisine: American
Did you like this recipe?Please comment, rate and share! And donโ€™t forget to tag me on Instagram @foxandbriar AND #foxandbriar so I can see what you made!
Hello! I’m Meghan.

I am so glad that you are here! I am the recipe developer, photographer, and writer here at my blog Fox and Briar. I am a passionate, self-taught home cook and believe that most things are better homemade and that good food doesnโ€™t need to be complicated.

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