Paleo Pumpkin Zucchini Muffins

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This Paleo pumpkin zucchini muffins recipe is a healthy breakfast that’s easy to make. These muffins are gluten-free, dairy-free and can easily be made into healthy pumpkin zucchini bread!

Front view of 5 Paleo Pumpkin Zucchini Muffins with chocolate chips


Summer and fall produce collide to make these delicious Paleo Pumpkin Zucchini Muffins!

Loaded with veggies, these muffins are gluten-free, grain-free, dairy-free and paleo. So they are a delicious breakfast everyone can enjoy.

They are moist with cozy fall spices and a perfect crumb, and so easy to make!

front view of a stack of three Pumpkin Zucchini Muffins, the top one has a bite taken out of it

Paleo Pumpkin Zucchini Muffins: Ingredients & Substitutions 

I really do not recommend making any substitutions in this recipe! Especially do not tamper with the kind and amount of flour. Paleo baking is a fine art, and I changing the flours in any way may result in a not-so-great muffin!

Overhead view of the ingredients in this healthy pumpkin zucchini muffins recipe
  • Pumpkin puree. Homemade pumpkin puree or canned can be used in this recipe.
  • Apple cider vinegar. white vinegar is a good substitute.
  • Coconut sugar. Any granulated sugar works well in this recipe. Just be sure to choose a variety that complies with your dietary needs.
  • Coconut oil. Butter or ghee are tasty substitutes for coconut oil.
  • Chocolate chips. These can be left out entirely. Also feel free to substitute your favorite chip variety, cinnamon, white chocolate, butterscotch, caramel, peanut butter, the sky’s the limit! For a paleo variety try these Enjoy Life Foods morsels.
  • Pumpkin Pie Spice. Use store bought or make your own with this recipe: homemade pumpkin pie spice.
overhead view of 8 Paleo Pumpkin Zucchini Muffins or Bread

How to Make Pumpkin Zucchini Muffins

These pumpkin zucchini muffins are a breeze to make! So let’s walk through the process together

Start by adding the pumpkin and the zucchini and blending until smooth (preferably in a high-powered blender like a Vitamix). This will ensure the zucchini is completely blended (see the photo on the right below, it’s undetectable.

Next, add the dry ingredients and blend until combined! As you can see in the middle photo, the batter gets pretty thick (which is how it should be).

So you may need to scrape the sides and keep blending until the mixture is well mixed.

Paleo Pumpkin Zucchini Muffins  batter in a blending container

Chocolate chips are optional (I guess)! But if you would like to add them be sure to stir them into the batter by hand (do not blend).

adding chocolate chips to Paleo Pumpkin Zucchini Muffins batter in a blending container

Bake

I recommend using a nonstick muffin tin to bake these Pumpkin Zucchini Muffins. Such a pan crisps the outsides beautifully. Please do not use muffin liners because they are difficult to remove from the baked muffins.

Grease the muffin pan well using your favorite method. Use a ¼ cup measuring cup to fill the wells of a standard muffin tin with the pumpkin zucchini muffin batter. The wells should be filled about ¾ full to prevent the muffins from overflowing.

Up close overhead view of a muffin pan filled with Pumpkin Zucchini Muffins batter before being baked.

Once you have finished filling the muffin tin, bake the Pumpkin Zucchini Muffins in the preheated oven. The muffins are done when the tops have set and spring back when touched.

overhead view of a muffin pan with Pumpkin Zucchini Muffins in it just after baking

Cool

Let the muffins cool in the pan for about 5 to 10 minutes before removing them and transferring them to a wire rack to cool the rest of the way.

Use a spoon or knife to release the edges of the pumpkin zucchini muffins from the pan before removing them completely. This will ensure they hold their shape well!

Serve

Serve slightly warm with a spread of almond butter, honey butter, apple butter, or pumpkin butter. Or, alongside your favorite breakfast recipes.

Up close overhead view of Pumpkin Zucchini Muffins on a cooling rack

Store/Freeze

Store leftovers in an airtight container in the refrigerator for up to 1 week.

These healthy Pumpkin Zucchini Muffins also freeze well. Make sure they are cooled completely, then put them in a ziplock bag or freezer-friendly container and store them in the freezer for up to 2 months.

To eat, simply reheat in the microwave for about 30-60 seconds (depending on the number of muffins), or warm in the oven!

5 Paleo Pumpkin Zucchini Muffins

Paleo Pumpkin Zucchini Muffins Recipe FAQs

Do I need to shred the zucchini?

I just chopped the zucchini into large pieces because the Vitamix makes it undetectable. However, for measuring purposes I recommend chopping or shredding the zucchini so you use the correct amount.

Can I make this into pumpkin zucchini bread?

This recipe can easily be made into bread. Simply bake the batter in a 9×5″ or 8×3″ pan for 35-45 minutes at 350 degrees F!
I recommend lining the loaf pan with aluminum foil and then greasing the foil for easy removal! Let the bread cool in the pan for at least 10 minutes before removing.

Overhead view of a Pumpkin Zucchini Muffin with a bite taken out of it so you can see the melty chocolate on the inside

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Paleo Pumpkin Zucchini Muffins Recipe

Laura
This Paleo pumpkin zucchini muffins recipe is a healthy breakfast that's easy to make. These muffins are gluten-free, dairy-free and can easily be made into healthy pumpkin zucchini bread!
4.95 from 17 votes
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 126
Prep Time5 minutes
Cook Time25 minutes
Total Time30 minutes

Ingredients 
 

Instructions 

  • Preheat the oven to 375 degrees F. Grease a standard muffin pan, set aside.
  • Combine coconut flour, almond flour, cinnamon, pumpkin pie spice baking soda, baking powder and salt in a small bowl, set aside.
  • Put zucchini, pumpkin, coconut sugar, and coconut oil into a blending container or food processor fitted with an "S" blade, and blend or process until smooth.
  • Add the vanilla and apple cider vinegar and blend or process until combined.
  • Add the dry ingredients and blend until combined.
  • Add eggs all at once and blend until just combined.
  • Mix in chocolate chips (or cinnamon chips) by hand.
  • Scoop ¼ cup portions of batter into each well of the prepared muffin pan.
  • Bake for 20-25 minutes until a toothpick inserted into the center of each muffin comes out clean. (To make into bread bake in 9×5” loaf pan for 35-40 minutes!)

Video

Notes

Ingredient Substitutions
  • Pumpkin puree. Homemade pumpkin puree or canned can be used in this recipe. Please be sure to use a pure variety that has only one ingredient: pumpkin. Do not use pumpkin pie filling.
  • Coconut sugar. Any granulated sugar works well in this recipe. Just be sure to choose a variety that complies with your dietary needs.
  • Coconut oil. Butter or ghee are tasty substitutes for coconut oil.
  • Chocolate chips. These can be left out entirely. Also feel free to substitute your favorite chip variety, cinnamon, white chocolate, butterscotch, caramel, peanut butter, the sky’s the limit! For a paleo variety try these Enjoy Life Foods morsels.
  • Pumpkin Pie Spice. Use store bought or make homemade pumpkin pie spice!
Make into Bread
These healthy pumpkin muffins can easily be made into pumpkin zucchini bread! Simply bake the batter in a 9×5″ or 8×3″ pan for 35-45 minutes at 350 degrees F! 
Store/Freeze
Store leftovers in an airtight container in the refrigerator for up to 1 week.
These healthy Pumpkin Zucchini Muffins also freeze well. Make sure they are cooled completely, then put them in a ziplock bag or freezer-friendly container and store them in the freezer for up to 2 months.
To eat, simply reheat in the microwave for about 30-60 seconds (depending on the number of muffins), or warm in the oven!

Nutrition

Serving: 1muffin | Calories: 126kcal | Carbohydrates: 13.7g | Protein: 4g | Fat: 6.8g | Saturated Fat: 3.4g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 1g | Cholesterol: 62mg | Sodium: 184mg | Potassium: 77mg | Fiber: 3.7g | Sugar: 8g | Vitamin A: 2750IU | Vitamin C: 1.4mg | Calcium: 30mg | Iron: 0.8mg

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

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Recipe Rating




90 Comments

  1. 5 stars
    We’re on our second double batch of these muffins! We used the food processor to make them and it worked perfectly! Such a breeze and sooo good! We’re mixing cinnamon and chocolate chips and they sound tasty!

  2. Do you think the recipe would still work if substituted the coconut sugar with honey or maple syrup?

    1. It might be a little too moist, you might want to add an extra TBS or two of almond flour if you try that substitution.

  3. 5 stars
    Those are by far the best “healthy” muffins I made so far. I make a batch and send one a day in my daughters lunch box and it’s the only muffin she never return home.

  4. 5 stars
    Thanks for another gf recipe. I love how detailed all your recipes and comments are. Will try this soon!

  5. 5 stars
    These are amazing!! Pumpkin + chocolate (and zucchini)…one of the best combos! It’s either muffins or smoothies for breakfast every day, so I loved this pumpkin version! Will make again.

    1. Yes! They would NOT turn out at all! Coconut flour absorbs significantly more liquid than almond flour. Without the coconut flour you would be left with a mushy muffin mess! If you don’t have coconut flour I recommend trying a different recipe!