These healthy muffins are made with wholesome ingredients and warm fall spices, and have a really nice moist texture. You can find all of the ingredients at your local grocery store.

The only difference between these and traditional pumpkin muffins is that I used cassava flour instead of regular wheat flour, coconut oil instead of butter or vegetable oil, and stevia instead of sugar.

These muffins are paleo diet friendly, gluten-free, dairy free and can be made vegan, AIP and elimination diet friendly with the dietary modifications listed below!

Pumpkin muffins on wire cooling rack

Recipe ingredient substitutions

Cassava flour substitutions: Instead of cassava flour, you could also use other grain free flours such as tigernut flour, almond flour / almond meal, tapioca starch / arrowroot starch, or half almond flour and half coconut flour.

Baking soda substitutions: Instead of using 1 teaspoon of baking soda, you can use 2 teaspoons of baking powder.

Ground cinnamon, cloves and nutmeg substitutions: Instead of adding cinnamon, cloves and nutmeg individually, you can swap it out for 1.5 teaspoons of pumpkin pie spice.

Egg substitutions: Instead of regular eggs, swap it out for chia, gelatin or flax eggs.

Melted coconut oil substitutions: Instead of coconut oil, you could also use melted vegan butter or regular butter if you tolerate dairy.

Vanilla extract substitutions: Instead of liquid vanilla extract, you can also use ground vanilla beans or vanilla bean paste.

Pure pumpkin purée substitutions: Instead of using pure pumpkin puree, you can also use pumpkin pie filling. If you do this though, these muffins will be a lot higher in sugar. Omit the pumpkin spice because the pie filling will already have it.

Stevia powder substitutions: Instead of powdered stevia, swap it out for liquid stevia drops. Alternatively, you can use monk fruit extract or a sugar free alternative such as erythritol or xylitol.

Recipe variations

Add additional flavours: To spice things up, consider adding chocolate chips or a streusel topping.

Make this recipe sweeter: These muffins are sweetened only with stevia, but if you want to sweeten them up consider adding a little bit of coconut sugar, maple syrup, or honey. Avoid using refined sugar if you want to keep it paleo!

A pumpkin muffin placed on a decorative ceramic cup cake stand

Dietary modifications

Make this recipe vegan: To make vegan pumpkin muffins, simply omit the eggs and swap them out for chia or flax egg alternatives.

Make this recipe AIP friendly: Omit the eggs and swap them out for gelatin eggs. Omit the nutmeg.

Make this recipe elimination diet friendly: Omit the eggs and swap them out for either flax, chia or gelatin eggs.

Meal prep this recipe

These muffins make a great snack throughout the week. Freeze 2 muffins in each of 6 airtight containers and take 1 container out to thaw in the fridge each day. This will give you snacks for 6 days.

Storage tips

Store your muffins in an airtight container for up to 1 week in the fridge, or for up to 3 – 6 months in the freezer. 

Tried my healthy pumpkin muffins recipe?

Please leave me a rating and review below, and post a picture of the dish to Instagram and tag me at @foodsnfeels 🙌

You might also like:

If you liked this recipe, check out my other paleo muffins:

I also have a lot of other paleo recipes on my blog.

If you are looking for more, download one of my free seven day meal plans!

Pumpkin muffins in muffin tin beside a bowl of spices

Paleo Pumpkin Muffins (Gluten Free)

Tara Klippert
These healthy muffins are made with wholesome ingredients and warm fall spices, and have a really nice moist texture.
No ratings yet
Prep Time 15 minutes
Cook Time 30 minutes
Total Time 45 minutes
Course Breakfast, Snack
Cuisine American
Servings 12
Calories 160 kcal



  • Preheat your oven to 350F.
  • In your KitchenAid stand mixer or large bowl, mix together all of your dry ingredients including cassava flour, baking soda, salt, cinnamon, cloves, nutmeg and stevia powder.
  • Next add all of your wet ingredients to your dry ingredients including pumpkin purée, melted coconut oil, eggs and vanilla extract.
  • Blend everything together thoroughly until no lumps remain.
  • Line your muffin tin with 12 muffin cups (I prefer the parchment paper ones but you can also use silicone muffin cups).
  • Evenly distribute your muffin batter into your muffin pan.
  • Bake your muffins for 30 minutes or until a toothpick comes out clean.



Above in the blog post I provide recipe ingredient substitutions and variations, dietary modifications, and storage tips.


Calories: 160kcalCarbohydrates: 15gProtein: 2.3gFat: 10.5gSaturated Fat: 8gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 1gTrans Fat: 0gCholesterol: 46.5mgSodium: 308mgFiber: 2.5gSugar: 1g
Keyword dairy free, gluten free, grain free, Low FODMAP, nut free, paleo, soy free, sugar free
Tried this recipe?Let us know how it was!

Disclaimer: This recipe post contains Amazon affiliate links. This means that if you click on a link and make a purchase, I will receive a small commission (at no extra cost to you). This helps support me so that I can continue to put out high quality, free recipes for you guys! Thank you 😁🙌

Tara Klippert
About the author Tara Klippert

Tara Klippert is a Registered Health and Nutrition Counselor and holds a diploma in Holistic Nutrition and Health Coaching. She shares her gluten free, dairy free & allergy friendly recipes.