Capture the delicious transition from late summer to early autumn with a muffin that does it all! This recipe for Healthy Pumpkin Zucchini Muffins combines the last of the summer zucchini harvest with the cozy, spiced flavor of fall pumpkin. The result is an incredibly moist, fluffy, and light muffin that’s bursting with flavor. Best of all, this recipe is designed to be allergen-friendly—it’s naturally gluten-free, dairy-free, and sweetened with maple syrup. It’s the perfect wholesome breakfast or snack the whole family will love.

Why You’ll Be Making These All Season Long

This isn’t just another muffin recipe; it’s a game-changer for healthy baking. Here’s why:

Perfectly Moist & Fluffy: A unique high-temperature baking start gives these muffins a beautiful bakery-style dome, while the pumpkin and zucchini ensure a tender, moist crumb.
Allergen-Friendly: This recipe is thoughtfully crafted to be gluten-free and dairy-free, making it a safe and delicious choice for those with dietary restrictions.
Wholesome & Naturally Sweetened: Forget refined sugar. These muffins get their delightful sweetness from pure maple syrup, plus natural sweetness from the pumpkin itself.
Packed with Fall Flavor: Loaded with pumpkin spice, every bite tastes like a cozy autumn day.

Your Wholesome Ingredient Checklist

Gather these simple, healthy ingredients to create a batch of these amazing muffins.

Dry Ingredients:

1 cup 1-to-1 gluten-free baking flour
1 tablespoon pumpkin pie spice
1 teaspoon baking soda
¼ teaspoon baking powder
¼ teaspoon sea salt

Wet Ingredients:

1 cup pumpkin puree (not pumpkin pie filling)
¾ cup shredded zucchini (from about 1 medium zucchini, moisture squeezed out)
½ cup coconut oil, melted and cooled slightly
½ cup pure maple syrup
2 large eggs, beaten

Fun Add-ins:

⅓ cup chocolate chips (use a dairy-free brand like Enjoy Life to keep the recipe dairy-free)

Step-by-Step Guide to Baking Perfection

This recipe uses a special two-temperature baking method for the best texture. Don’t be intimidated—it’s easy!

Part 1: Prepping and Mixing

Prep the Zucchini: First, shred your zucchini. Place the shreds in a clean kitchen towel or paper towels and squeeze firmly to remove as much excess water as possible. This is a crucial step for the best texture!
Preheat and Prepare Pan: Preheat your oven to 425°F (220°C). Line a standard 12-cup muffin tin with paper or silicone liners. For best results, lightly spray the inside of the liners with cooking spray to prevent sticking.
Mix Dry Ingredients: In a large bowl, whisk together the gluten-free flour, pumpkin pie spice, baking soda, baking powder, and sea salt.
Mix Wet Ingredients: In a separate medium bowl, combine the pumpkin puree, squeezed zucchini, melted coconut oil, maple syrup, and beaten eggs. Stir until everything is well incorporated.
Combine and Fold: Pour the wet ingredients into the bowl with the dry ingredients. Mix with a spatula until just moistened. Lumps are okay! Do not overmix. Gently fold in the chocolate chips.

Part 2: The Two-Temp Baking Method

Fill Muffin Cups: Use a standard ice cream scoop to divide the batter evenly among the 12 muffin cups. They should be about ¾ full.
Initial High-Temp Bake: Place the muffins in the 425°F oven and bake for 5 minutes. This initial blast of high heat helps the muffins rise quickly and form a beautiful dome.
Lower Temp and Finish Baking: Keeping the muffins in the oven, reduce the oven temperature to 350°F (175°C). Continue baking for another 15-20 minutes. The muffins are done when a toothpick inserted into the center comes out clean.
Cool Completely: Let the muffins cool in the pan for 10 minutes before carefully moving them to a wire rack to cool completely. Allowing them to cool fully is important for the best texture.

Expert Tips & Delicious Variations

Make it Vegan: To make this recipe vegan, simply substitute the 2 large eggs with 2 “flax eggs.” To make a flax egg, mix 1 tablespoon of ground flaxseed with 3 tablespoons of water and let it sit for 5 minutes to thicken.
Other Fun Mix-ins: Not a fan of chocolate chips? Try folding in ⅓ cup of chopped walnuts, pecans, or dried cranberries (Craisins) instead.
The No-Stick Trick: Gluten-free muffins can be sticky. Using silicone liners is a great option, but if you use paper liners, a light spritz of cooking spray inside them works wonders.
Storage Instructions: Store the cooled muffins in an airtight container. They will last for up to 2 days at room temperature, up to 5 days in the refrigerator, or can be frozen for up to 3 months for a quick future snack.

Expand your zucchini repertoire with these favorites:

The Ultimate Oat Flour Zucchini Bread Recipe: Healthy, Moist & Delicious
Zucchini Pancake Recipe: Fluffy Green Pancakes in 15 Minutes
Easy Lemon Zucchini Bread Recipe: Moist, Citrusy, and Irresistible
The Ultimate Zucchini Breadwich: A Revolutionary Low-Carb Sandwich

Healthy Gluten-Free Pumpkin Zucchini Muffins

Moist, fluffy, and perfectly spiced, these gluten-free and dairy-free muffins combine pumpkin and zucchini for a nutritious fall treat sweetened with pure maple syrup.

Print Recipe Pin Recipe

Prep Time 15

Cook Time 25

Total Time 40

Course Breakfast, Snack

Cuisine Dairy-Free, Gluten-Free, Healthy

Servings 12 muffins

Ingredients

Dry Ingredients

1 cup 1-to-1 gluten-free baking flour
1 tablespoon pumpkin pie spice
1 teaspoon baking soda
1/4 teaspoon baking powder
1/4 teaspoon sea salt

Wet Ingredients

1 cup pumpkin puree not pumpkin pie filling
3/4 cup shredded zucchini moisture squeezed out
1/2 cup coconut oil melted and cooled slightly
1/2 cup pure maple syrup
2 large eggs beaten

Fun Add-ins

1/3 cup chocolate chips use dairy-free if needed

Instructions

Preheat oven to 425°F (220°C) and line a 12-cup muffin tin with liners. Lightly spray liners with cooking spray if using paper.
Shred zucchini and squeeze out excess moisture using a kitchen towel or paper towels. Set aside.
In a large bowl, whisk together the gluten-free flour, pumpkin pie spice, baking soda, baking powder, and salt.
In a medium bowl, mix together pumpkin puree, squeezed zucchini, melted coconut oil, maple syrup, and beaten eggs until fully combined.
Add the wet mixture into the dry ingredients. Stir gently until just combined. Do not overmix.
Fold in chocolate chips.
Divide batter evenly among the muffin cups, filling each about ¾ full.
Bake at 425°F (220°C) for 5 minutes, then without opening the oven, reduce heat to 350°F (175°C) and continue baking for 15–20 minutes until a toothpick inserted comes out clean.
Cool muffins in the pan for 10 minutes before transferring to a wire rack to cool completely.

Notes

Make it vegan by substituting eggs with flax eggs. Use chopped nuts or cranberries instead of chocolate chips. Store in an airtight container for up to 5 days in the fridge or freeze for 3 months.