The Best Healthy Pumpkin Muffins (Vegan & Gluten-Free)

These healthy pumpkin muffins are the perfect fall bake! Simple ingredients like oat flour, pumpkin puree, and the easiest healthy streusel topping make light and fluffy muffins packed with pumpkin flavor. They're also vegan, gluten-free, oil-free, and refined-sugar-free.

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Although you can make these tender vegan pumpkin muffins any time of the year, there is no better time than now, with pumpkin season just around the corner. These muffins are super easy to make, plant-based, and gluten-free. They are topped with a flavorful streusel that adds the perfect amount of sweetness—all-refined sugar-free. Enjoy them for breakfast, a quick snack, or a healthy sweet treat.

looking down at the pumpkin muffins turned on its side with pumpkins and streusel around it

Yep, it's official. The cooler weather has rolled in. Even grocery stores have changed their display to make fresh pumpkins, pumpkin pie spice, or anything with a pumpkin spice flavor front and center. No wonder I crave all things pumpkin. From my Pumpkin Hot Chocolate to Vegan Pumpkin Bread Pudding, I am going to make them all again this season. But what's missing on the blog are fluffy vegan pumpkin muffins to complete fall's cozy, comforting flavors. Well, until now.

I've tested these numerous times to get the flavors right, and I think I've finally got a winner. I hope you like them as much as I do. The best part is that they're also super easy to make. I also used Good Karma Oatmilk + Barista Blend in this recipe, which made the muffins extra moist. (While this post isn’t sponsored, and you can, of course, use other plant-based milk to make this recipe, I highly recommend their oat milk for the best results!). Let's make some amazing muffins.

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Ingredients To Make The Best Vegan Pumpkin Muffins:
How to Make These Amazing Muffins:
Top Tips:
Substitutions:
Variations:
Equipment You Need To Make These Pumpkin Muffins:
Storage:
Recipe FAQs:
More Pumpkin Recipes You Might Like:
The Best Healthy Pumpkin Muffins (Vegan & Gluten-Free)
More Vegan Recipes For Fall:

Ingredients To Make The Best Vegan Pumpkin Muffins:

I know what you're thinking: that's a long ingredient list. But I promise you, as soon as you've gathered the ingredients, everything comes together rather quickly. Plus, if you're familiar with baking my vegan goods, you have most of these ingredients already on hand. And there is nothing you can't buy either at your local grocery store or online. I have included all the direct online links to where to get some of my "secret" ingredients, and you can take advantage of my discount codes. So let's have a look!

Note: If you plan to purchase any of the Wilderness Poets products, use my code “NATURALVEGAN” to get $10 off any purchase of $49 or more.

the healthy vegan pumpkin muffin with streusel on top

Maple Crystals: This is my all-time favorite sweetener, and I use it in many of my baked goods, like my Gluten-Free Vegan Pistachio Cookies or Maple Candied Pecan Cookies. It's a much healthier alternative to most sugars, yet it gives these muffins a rich sweetness without spiking your blood sugar as much. What's not to love?
Flour: I use a good blend of oat flour and gluten-free flour ( I always recommend using this one for best results). Both keep these muffins light and fluffy, while the oat flour also adds a wholesome, nutty flavor. Make sure you use a gluten-free option.
Leavening Agents: I use a combo of baking powder and baking soda to give these egg-free pumpkin muffins that beautiful lift.
Vanilla bean powder: It adds a super rich vanilla flavor, just like in my Bakery-Style Gluten-Free Vanilla Muffins. This Wilderness Poets product is one of my favorites for adding warmth and a depth of flavor to my vegan baked goods. I highly recommend investing in this powder. I always have a small jar in my pantry, and a little goes a long way. Use my discount code above and see what a difference it makes when you bake with it.
Flax Egg: I use ground flax seeds and water to make a flax egg. It helps bind the ingredients together, making these muffins vegan without sacrificing their fluffy texture.
Vegan Yogurt: I recommend coconut yogurt for a softer texture.
Pumpkin Puree: Make sure you use pure pumpkin puree, not pumpkin pie filling. You don't need a whole can of pumpkin puree so use any leftovers to make extra Pumpkin Hot Chocolate Drinks.
Good Karma Barista Blend Oat Milk: This oat milk adds the perfect creaminess and moisture to the muffins. If you’re not using Good Karma, feel free to substitute any plant-based milk.
Apple Cider Vinegar: You need a little acid to enhance the flavors and allow the muffins to rise.
Vanilla Extract: Some is added to both the muffin batter and the topping for a richer flavor and a caramel-like touch.
Coconut Butter: I'm warming it up to make it smooth and liquid. This healthy fat adds a delicious creamy texture to the topping.
Cinnamon: I'm only using a tad to flavor the topping and add some extra fall flavors. It's one of those fall spices you probably already have on hand, and you should definitely use it to make my Gluten-Free Cinnamon Raisin Muffins and Vegan Protein Cinnamon Rolls next.
Pumpkin Seeds: These add a nice crunch and make the muffins look extra pretty!

See the recipe card for quantities.

How to Make These Amazing Muffins:

As I've mentioned before, it's super easy. In a few steps, these Healthy Pumpkin Muffins are ready to be baked.

Prepare the Flax Egg: Combine the ground flax seeds and water in a small bowl. Stir and let it sit for 5-10 minutes to thicken.
Mix Dry Ingredients: In a large bowl, whisk together the oat flour, gluten-free flour, leavening agents, and vanilla bean powder if using.
Mix Wet Ingredients: In a separate bowl, combine the vegan yogurt, plant-based milk, apple cider vinegar, pumpkin puree, and vanilla extract.
Bring It All Together: Gradually stir the wet ingredients into the dry ones until just combined. Fold in the flax egg until well incorporated.
Add the Streusel Topping & Bake: In a small bowl, mix the topping ingredients with water until you get a crumbly concoction. Spoon the batter into the prepared muffin tin, filling each cup about ¾ full. Sprinkle the streusel topping evenly over the muffin batter. Bake in a preheated oven until a toothpick inserted comes out clean.
Cool and Serve: Let the muffins cool in the muffin tin for 5 minutes before transferring them to a cooling rack to cool completely. Serve and enjoy!

Top Tips:

Although this is a simple vegan pumpkin muffin recipe, here are a few recommendations for making the best fall-flavored muffins.

Don't Overmix: As with almost all my vegan muffins, it's best not to overmix wet with dry ingredients to avoid a dense texture. And always make sure there are no lumps left in the batter.
Use Room-Temperature Ingredients: For the best texture, make sure your wet ingredients, such as plant-based milk and vegan yogurt, are at room temperature.
Measure: Use measuring cups and spoons to get the exact amount of ingredients. You want your muffin batter to have the right balance of texture and flavor.
Ice Cream Scoop: To evenly distribute the muffin batter into the muffin cups, use an ice cream or cookie scoop—optional!

Substitutions:

As with all my muffin recipes, I first encourage you to make the recipe as-is because I've already tested it numerous times, so you don't have to. However, there are a few substitutions that can work. Let's have a look.

Alternative Sweeteners: Although I prefer Maple Crystals, you can substitute them with brown or coconut sugar.
Alternative Flours: If gluten is not an issue for you, try using all-purpose flour or opt for regular whole wheat flour or whole wheat pastry flour instead of the gluten-free blend for a heartier texture. Please note that texture and taste will vary based on what flour you use.
Oat Milk Alternative: I highly recommend the Good Karma Barista Blend Oat Milk, but nut milk can work.

looking down at the muffin with a bite taken out of it to show the fluffy texture

Variations:

Chocolate Chips: For an extra indulgence, fold some vegan chocolate chips into the batter for pumpkin chocolate chip muffins. A little chocolate has never ruined a pumpkin muffin. I love using these ones from Wilderness Poets because they are naturally sweetened and vegan!
Make Mini Muffins: You can use a mini muffin pan to make bite-sized versions. This will probably reduce the baking time to about 15-18 minutes.

Equipment You Need To Make These Pumpkin Muffins:

Here's what you need to gather from your kitchen to make these delicious muffins.

Whisk: To fluff up the flour and combine the dry ingredients.
6-count muffin tin or 12-count Muffin Tin: A standard muffin pan is perfect for this recipe. For easy removal, you can use paper or muffin liners instead of oiling the muffin cups.
Mixing Bowls: You need a few mixing bowls to mix the dry ingredients, make the flax egg, combine the wet ingredients, and make the streusel topping.
Wire Rack or Cooling Rack: Essential for cooling the muffins evenly.
Ice Cream Scoop (optional): To ensure even-sized muffins.
Measuring Spoons and Cups: These are used to measure ingredients accurately.
Wooden Spoons: To combine.

Storage:

Store leftover pumpkin muffins in an airtight container at room temperature for up to 3-4 days, or freeze them for up to 3 months. If you plan to freeze then, place them in a sealed container or freezer-safe bag first. Defrost them for a couple of hours before serving. I love to warm them up by popping them for 20 seconds in the microwave (optional).

Recipe FAQs:

Can I use homemade pumpkin puree?

Absolutely! Homemade pumpkin puree will give these muffins an even richer pumpkin flavor. Just make sure to use a smooth puree for the best results.

Can I use spelt flour?

Spelt flour is not a good substitute to replace gluten-free flours because it contains gluten. If that's not a concern, spelt flour can be a great substitute in general. I use it to make my Healthy Coffee Cake, Vegan Chocolate Loaf Cake, or Cranberry Orange Muffins. If you use Spelt flour to make these Vegan Pumpkin Muffins, be sure to let me know in the comments.

More Pumpkin Recipes You Might Like:

Looking for other vegan pumpkin recipes like these vegan pumpkin muffins? Try these:

These easy vegan pumpkin muffins are the ultimate fall treat, perfect for cozy mornings or as a healthy, sweet baked good any time of day. They’re a must-try!

If you try these Healthy Vegan Pumpkin Muffins, I’d really love to hear your thoughts in the comments below. I’d also really appreciate a recipe card rating! Make sure to share it on social media and tag @theallnaturalvegan to be featured! Thank you for supporting The All Natural Vegan!