I’m so excited to share the best pumpkin muffins with you! These beautiful pumpkin muffins are light, soft, and just sweet enough. They are gluten-free thanks to natural whole food flours, but you’d never know it by tasting them. They are also dairy-free, egg-free, and vegan. 

These amazing healthy pumpkin muffins are vegan and gluten-free! Made with a little coconut oil and maple syrup, they are low sugar and low fat.

The time has come! I can wait no longer to share the first pumpkin recipe of the season, and the BEST muffins of the season! I’ve posted pumpkin muffins in the past, like Grain-Free Paleo Pumpkin Muffins , Healthy Pumpkin Muffins. And plenty of pumpkin recipes, like Vegan Pumpkin Bread, Vegan Pumpkin Pie, Vegan Pumpkin Cheesecake, Vegan Pumpkin Ice Cream and last year’s crazy but delicious Pumpkin Pie Hummus!

One afternoon this week my daughter and I worked on this easy and healthier recipe for gluten free and vegan pumpkin muffins. It took three attempts, but we finally nailed it. These pumpkin muffins are light and soft, and incredibly delicious on their own, or with nuts and cranberries mixed in, or topped with frosting.

Oat flour, almond flour, and tapioca flour in a bowl to make gluten free pumpkin muffins.

Gluten-Free Flour for Muffins

My Gluten Free Blueberry Banana Oat Muffins continue to get such lovely reviews that I knew I wanted to adapt it for the fall season by swapping out the banana for the pumpkin. The first attempt used 100% oat flour, and while we really enjoyed them, we wanted them to be lighter and fluffier.

For the next attempt we made a blend with oat flour, almond flour, and tapioca flour (tapioca starch). Almond flour ads structure while tapioca flour ads lightness. This blend resulted in a much lighter muffin. We preferred the texture of the blend, but if you like dense muffins or only have oats/oat flour, you can use that. If you’re making these muffins for kids at school I would recommend using only oat flour to keep them allergy-friendly.

Are Oats Gluten-Free?

Oats are naturally gluten free but often contaminated during processing. It’s important to choose certified gluten free oats if you have an intolerance. If you’re in Australia, you may not be able to find gluten free oats. I make my own oat flour by blending oats in the blender until finely ground.

Pumpkin puree mix and gluten free flour blend in two bowls ready to mix together for pumpkin muffins.

How to Make Vegan Pumpkin Muffins

Mix the wet and dry ingredients together in two separate bowls. I add the flax meal to the “wet” ingredient bowl so that it can thicken up and act as a binder.

Use unsweetened pumpkin puree rather than pumpkin pie filling. I used the organic canned pumpkin from Trader Joe’s.

Wet pumpkin muffin ingredients are added to dry flour ingredients.

The pumpkin puree gets naturally sweetened with maple syrup and flavor boost from vanilla extract.

Vegan gluten free pumpkin muffin batter ready for the muffin pan.

Fold the wet and dry ingredient blends together gently until just combined.

Fresh cranberries get folded into vegan pumpkin muffin batter for muffins.

Pumpkin Muffin Variations and Mix-ins

Pumpkin muffins are perfect plain, but I think they are even more delicious with additions. Here are some of my favorite ingredients to mix in.

  • chocolate chips
  • chopped pecans
  • chopped walnuts
  • fresh or frozen cranberries

Pumpkin muffins in a tin with fresh cranberries and pepitas. These deliciously healthy pumpkin muffins are vegan and gluten free.

Fresh or frozen cranberries add a wonderful tart and juicy element to these warm spiced muffins. While fresh cranberries are only available for a couple of months around the holidays, you can often find them with the frozen fruit. I use them in this Cranberry Smoothie year-round. Pepitas (pumpkin seeds) work well here as a fun crunchy topping. They’re really good for you, too.

A small bowl of cinnamon dairy-free vegan cream cheese frosting for pumpkin muffins.

Do you remember those Gluten Free Vegan Carrot Muffins from a few months ago? They had the most delicious cream cheese frosting! Knowing how well cream cheese and pumpkin muffins pair, I had to try that frosting on a few of these muffins.

A beautiful photo of making gluten free vegan pumpkin muffins with dairy-free cinnamon cream cheese frosting with pepitas.

These amazing healthy pumpkin muffins are vegan and gluten-free! Made with a little coconut oil and maple syrup, they are low sugar and low fat.

Yield: 12 muffins

Gluten-Free Pumpkin Muffins

Prep Time 5 minutes
Cook Time 15 minutes
Total Time 20 minutes

These delicious pumpkin muffins taste like fall! Made with oat flour, almond, and tapioca flour, they are gluten-free, dairy-free, and vegan.

Gluten-Free Pumpkin Muffins


  • 1 cup oat flour
  • 1/2 cup almond flour
  • 1/2 cup tapioca flour
  • 1/2 teaspoon baking soda
  • 2 teaspoons baking powder
  • 1/4 teaspoon salt
  • 2 tablespoons pumpkin pie spice
  • 1 cup pumpkin puree
  • 2 tablespoons flax meal
  • 1/4 cup melted coconut oil
  • 1 teaspoon vanilla
  • 1/2 cup maple syrup or sugar
  • 1/4 cup pepitas (optional)
  • 1/2 cup dairy free cream cheese, room temperature
  • 1/4 cup dairy free butter, room temperature (I like Miyoko’s)
  • 1/2 teaspoon vanilla extract
  • 1 cup organic powdered sugar
  • pinch of ground cinnamon to taste


  1. Preheat the oven to 375 degrees F. Line a muffin tin with parchment liners.
  2. In a medium bowl, whisk together the oat flour, almond flour, tapioca flour, baking soda, baking powder, salt, and pumpkin pie spice. Set aside.
  3. In another medium bowl, whisk together the pumpkin puree, flax meal, coconut oil, vanilla, and maple syrup.
  4. Fold the wet ingredients into the dry ingredients. Fold in any extras like 1 cup chopped walnuts or pecans, or fresh/frozen cranberries.
  5. Use an ice cream scoop to fill a muffin tin lined with parchment cupcake liners. Sprinkle with pepitas. Bake for 15 minutes, or until a tester comes out clean.
  6. To make the frosting, place the cream cheese and butter into the bowl of a mixer. Beat on high speed until light and smooth. Beat in the vanilla, cinnamon, and powdered sugar to taste. If the frosting to thicker than you like, you can thin it with a few drops of almond milk. Spread on your muffins.


  1. If you only have oats, you can make these muffins with 2 cups of oat flour. They will be a little more dense, but still delicious.
  2. I love adding fresh or frozen cranberries and chopped walnuts to these pumpkin muffins.

Nutrition Information:
Yield: 12 Serving Size: 1
Amount Per Serving: Calories: 292Total Fat: 17gSaturated Fat: 9gTrans Fat: 0gUnsaturated Fat: 6gCholesterol: 20mgSodium: 244mgCarbohydrates: 33gFiber: 2gSugar: 19gProtein: 4g