These healthy pumpkin muffins are moist, fluffy, and perfectly spiced! Made in one bowl with oat flour, maple syrup, and melty chocolate chips. Vegan, gluten-free, & refined sugar-free.

overhead shot of healthy pumpkin muffins on a plate garnished with a cinnamon stick

It’s officially pumpkin season and I couldn’t be more excited! I’ve been sneaking pumpkin into everything lately: overnight oats, stuffed dates, banana bread, even energy balls.

But today? I woke up craving muffins. Not just any muffin. I wanted a soft, fluffy, perfectly spiced muffin that tastes like fall in every bite. And these are exactly that.

Featured Comment

Just made these today and they were delicious!!! The perfect balance of pumpkin and sweetness. My whole family loved them! The chocolate chips put them over the top!! I will be making these on repeat throughout the fall 🎃

— Lynda
6 more reviews »

Packed with warm pumpkin spices, gooey chocolate chips, and the most tender crumb, these pumpkin muffins are truly something to drool over. They’re made with healthier ingredients like oat flour, pumpkin puree, and naturally sweetened with a combo of maple syrup + coconut sugar.

Oh and, of course, they’re completely vegan, gluten-free, dairy-free, and refined sugar-free.

Just one bowl and about 20 minutes in the oven, and you’ll have the best healthy pumpkin muffins. Let’s dive in!

moist and fluffy pumpkin muffin cut in half to show soft crumb and melty chocolate chips

You guys…look at that interior. The moist, tender crumb + melty chocolate chips (crying emoji) they’re SO GOOD!

Why You’ll Love These Pumpkin Muffins

  • Bakery-level flavor: warm pumpkin spices, melty chocolate chips, and the softest crumb.
  • Soft & fluffy texture: moist, tender, and light without any eggs or dairy.
  • Wholesome ingredients: like oat flour, real pumpkin puree, and natural sweetness from maple syrup + coconut sugar.
  • One-bowl recipe: all the ingredients come together in one bowl (which means less clean up, too!).
  • Pumpkin goodness in every bite: if autumn were a muffin, it would taste just like this.
  • Vegan, gluten-free & naturally sweetened: proof that healthy baking can taste every bit as indulgent.

Ingredients Needed

Here’s everything you’ll need to make these healthy pumpkin muffins (most of which are probably already in your pantry!).

  • Oat Flour: gives these muffins their soft, fluffy texture while keeping them gluten-free. You can make your own by blending rolled oats into a fine flour. If you have a serious gluten allergy, be sure to use certified gluten free oats. I don’t recommend substituting for another type of flour, but if you try it, please let me know how it turned out in the comments!
  • Pumpkin Puree: the star of the show! Use pure pumpkin puree (not pumpkin pie filling).
  • Coconut Sugar: this natural sweetener adds a rich, caramel-like sweetness that pairs perfectly with pumpkin.
  • Non-Dairy Milk: any unsweetened non-dairy milk works here.
  • Maple Syrup: keeps the muffins moist and naturally sweet.
  • Coconut Oil: adds just the right amount of moisture. Use refined coconut oil so it doesn’t have any coconut flavor.
  • Vanilla Extract: an essential to add a hint of vanilla flavor.
  • Apple Cider Vinegar: reacts with the leavening agents to help the muffins rise.
  • Baking Powder & Baking Soda â€“ to help the muffins rise. It can be tricky to get vegan and gluten-free muffins to rise, so we have to use a bit more leavening agent to assist.
  • Spices: a mix of pumpkin pie spice, cinnamon, and salt
  • Chocolate Chips: optional but highly recommended. Pumpkin + chocolate = a dream team. I use these vegan chocolate chips.

How to Make Healthy Pumpkin Muffins

Scroll down to the recipe card to get the full recipe with measurements!

  1. Preheat the oven. Set the oven to 350°F and grease or line a muffin pan.
  2. Mix the wet ingredients. In a large bowl, whisk together the pumpkin puree, coconut sugar, non-dairy milk, maple syrup, coconut oil, vanilla extract, and apple cider vinegar.
  3. Add the dry ingredients. Stir in the oat flour, baking powder, baking soda, pumpkin pie spice, cinnamon, and salt until just combined. Fold in the chocolate chips.
  4. Fill the pan. Divide the batter evenly into the muffin pan and sprinkle with extra chocolate chips.
  5. Bake. Place in the oven and bake for 23–25 minutes, or until a toothpick comes out clean (a few crumbs are okay).
  6. Cool & enjoy. Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack.
freshly baked batch of vegan and gluten-free pumpkin muffins

Megan’s Tips

  • Use pumpkin puree, not pumpkin pie filing. They’ll look similar in the grocery store aisle, but pumpkin pie filling has added sugar and spices that will throw off the recipe.
  • Let the muffins cool. I know it’s tempting, but letting the muffins cool helps them set and avoids soggy bottoms.
  • Warm them up. Pop a muffin in the microwave for 10 seconds before eating; the chocolate chips get melty again and it’s pure heaven.

Serving Your Pumpkin Muffins

Here are a few of my favorite ways to enjoy them:

  • Warm with a little vegan butter (or nut butter) smeared on top
  • Paired with your morning coffee or my pumpkin spice chai latte
  • As an afternoon snack
  • For dessert with a scoop of ice cream

Basically, these vegan pumpkin muffins fit in anywhere: breakfast, snack, or sweet treat.

overhead shot of healthy pumpkin muffins on a plate garnished with a cinnamon stick

Frequently Asked Questions

Can I add nuts to these muffins?

Yes! Feel free to fold in chopped nuts for added texture and flavor. You can also make these muffins without the chocolate chips, but I highly recommend including them. Pumpkin + chocolate = a dream team.

How do I store pumpkin muffins?

Store the muffins in an airtight container at room temperature for 3-4 days. For longer storage, freeze them for up to 3 months.

Can I make my own pumpkin pie spice?

Definitely! If you don’t have pumpkin pie spice on hand, mix 1 teaspoon cinnamon with ½ teaspoon each of nutmeg, cloves, ginger, and allspice. You’ll be set for all your fall baking.

More Pumpkin Recipes You’ll Love

Find all of my pumpkin recipes here and more fall recipes here.

If you make this recipe, please be sure to leave a comment and ★★★★★ star rating below. Don’t forget to tag me on Instagram so I can see your creations!

freshly baked batch of vegan and gluten-free pumpkin muffins
5 from 3 ratings

Healthy Pumpkin Muffins (Vegan, Gluten-Free)

Megan Murphy
Yield: 12 muffins
Prep: 5 minutes
Cook: 25 minutes
Total: 30 minutes
These healthy pumpkin muffins are moist, fluffy, and perfectly spiced! Made in one bowl with oat flour, maple syrup, and melty chocolate chips. Vegan, gluten-free, & refined sugar-free.
Print Leave a Review Pin Recipe

Equipment

Ingredients
 

Wet Ingredients

Dry Ingredients

Instructions
 

  • Preheat the oven to 350°F and grease or line a muffin pan (I grease mine with coconut oil).
  • In a large bowl, whisk together the pumpkin puree, coconut sugar, non-dairy milk, maple syrup, melted coconut oil, vanilla extract, and apple cider vinegar.
  • Mix in the oat flour, baking powder, baking soda, pumpkin pie spice, cinnamon, salt. Fold in the chocolate chips.
  • Divide the batter evenly into the muffin pan and sprinkle with extra chocolate chips.
  • Bake for 20-25 minutes, or until a toothpick comes out clean (a few crumbs are okay).
  • Remove from the oven and let the muffins cool in the pan for 5 minutes, then transfer to a wire rack. Enjoy!

Video

Serving: 1muffin, Calories: 203kcal, Carbohydrates: 30g, Protein: 3g, Fat: 9g, Saturated Fat: 6g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Sodium: 202mg, Potassium: 131mg, Fiber: 2g, Sugar: 14g, Vitamin A: 3179IU, Vitamin C: 1mg, Calcium: 66mg, Iron: 2mg
Did you make this recipe?Tag @booboosbakeryy with hashtag #booboosbakery on Instagram. We love to see what you make!