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Home » Dessert » Gluten-Free Pumpkin Cupcakes (Vegan)

Gluten-Free Pumpkin Cupcakes (Vegan)

Published: Sep 25, 2025 by Rebecca Pytell · This post may contain affiliate links.

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The best Gluten-Free Pumpkin Cupcakes are vegan, allergy-free, and so easy to make! Made with real pumpkin and cozy spices, these moist and fluffy eggless pumpkin cupcakes are topped with a sweet and tangy dairy-free cream cheese frosting! Baked in 20 minutes with simple ingredients, everyone will love this homemade recipe!

gluten-free pumpkin cupcakes with vegan cream cheese frosting on plate.

From pumpkin cake to pumpkin cookies, there's nothing that can beat a light and fluffy bite of a perfectly spiced pumpkin cupcake with cream cheese frosting! Perfectly gluten-free and vegan, these cupcakes will steal the show at every fall and winter gathering you have on the calendar! Whether you're celebrating Halloween, Thanksgiving, seasonal classroom parties, or autumn birthdays, everyone can enjoy a warm and cozy pumpkin treat!

one gluten-free vegan pumpkin cupcake in wrapper on plate.

Why These Are The Best Pumpkin Cupcakes

Simple, delicious, packed with tons of real pumpkin and warming spices, these cupcakes are gluten-free, vegan, and allergy-free. The pumpkin allows you to use less oil, but still have an incredibly moist cake, which is essential when making gluten-free baked goods. Pumpkin also lets you keep these vegan pumpkin cupcakes naturally eggless! The pumpkin acts as a natural egg replacer (similar to banana). Plus, you can make these cupcakes sugar-free. Healthy? I'd say so! These homemade pumpkin cupcakes are:

  • Gluten-Free
  • Vegan & Vegetarian
  • Allergy-free (Dairy-Free, Soy-Free, Egg-Free, Nut-Free, Peanut-Free, Wheat-Free, Sesame-Free, Fish-Free, Shellfish-Free, Corn-Free, Coconut-Free)
  • Sugar-Free Option
  • Kid-Friendly & Customizable
  • Quick & Easy
  • Simple, Make-Ahead, & Freezer-Friendly
  • Perfect Fall Dessert For Any Occasion

Ingredients For Gluten-Free Vegan Pumpkin Cupcakes

ingredients for gluten-free vegan pumpkin cupcakes.

  • Gluten-Free All-Purpose Flour + Starch: Your favorite gluten-free all-purpose flour with an extra tablespoon of cornstarch (or arrowroot starch). This will give you cupcakes a perfect light and soft crumb!
  • Sweeteners: Using equal amounts of granulated sugar and rich molassesy dark brown sugar gives you just the right amount of sweetness that complements the pumpkin and spices. You can use sugar-free granulated sweetener and sugar-free brown sugar to keep the cupcakes sugar-free!
  • Baking Powder + Baking Soda + Salt: This baking trifecta adds to the fluffiness, leavening, and produces the perfect amount of air pockets when reacting to the acidic vegan buttermilk to make bakery-style cupcakes at home!
  • Pumpkin Spice: You can choose whichever cozy warming spices you'd like. Using all cinnamon is simple and delicious, but if you love "pumpkin spice", I suggest you use a pumpkin pie spice mix like my homemade one or a combo of nutmeg, ginger, allspice, and cloves.
  • Pumpkin Puree: This recipe uses 1 ½ cups of canned pumpkin. 100% real pumpkin flavor (make sure you use 100% pumpkin puree, not pumpkin pie filling!) adds natural moisture, binding, flavor, and color to the cupcakes!
  • Vegan Buttermilk: Plain unsweetened non-dairy milk plus a tablespoon of white vinegar (cider vinegar or lemon juice works too) mixed together and left to sit for 5 minutes before adding to the cupcake batter. However, you don't need much, and you will only use 3 tablespoons of vegan milk and 1 tablespoon of vinegar in this specific recipe. I kept them separate, as you may need more or less milk.
  • Oil: A neutral flavor oil, along with the pumpkin puree, keeps the gluten-free cupcakes super moist throughout. Gluten-free flours also need extra moisture, and since these cupcakes are eggless, the oil helps bind and hold the cake together. They won't stick to your cupcake liners either!
  • Vanilla Extract: Soft notes of vanilla will help the pumpkin flavor shine! You can also use some maple extract for even more fall-themed flavor!

Vegan Cream Cheese Frosting

For homemade vegan cream cheese frosting, you'll need vegan cream cheese, vegan butter, powdered sugar (or a sugar-free variety like Swerve), vanilla, and just enough water or plain non-dairy milk to help the mixture combine. Beat the mixture in a stand mixer, or a large bowl using a hand mixer, until smooth. Allow the frosting to chill in the fridge until you are ready to frost the cupcakes. You can also use store-bought vegan cream cheese frosting, or make a batch of simple vegan vanilla buttercream frosting instead!

How To Make Gluten-Free Pumpkin Cupcakes

steps 1 and 2 whisking together dry cupcake ingredients.

  1. Add the gluten-free flour, starch, baking powder, baking soda, salt, spices, granulated sugar, and brown sugar to a large mixing bowl.
  2. Whisk together the dry ingredients until fully combined.

steps 3 and 4 mixing together pumpkin mixture and adding to dry ingredients.

  1. In a small bowl, mix together the pumpkin, vinegar, vanilla, and oil.
  2. Add the wet pumpkin mixture to the dry ingredients.

steps 5 and 6 mixing in wet pumpkin ingredients to dry and adding vegan milk.

  1. Mix together the wet ingredients and dry ingredients until you have a slightly thick orange batter.
  2. Lastly, add the vegan milk. Mix until smooth, and no visible lumps or clumps of batter are showing.

steps 7 and 8 adding pumpkin batter to cupcake tin and baking.

  1. Line a standard 12-count cupcake tin with cupcake liners and fill each hole with about 3 tablespoons of pumpkin batter (about ¾ full) for 12 cupcakes.
  2. Bake the gluten-free pumpkin cupcakes in the oven for about 20 minutes, until the tops are round and golden.

steps 9 and 10 cooling cupcakes before frosting them.

  1.  Allow the cupcakes to cool completely on a wire rack before frosting them.
  2. Once the vegan pumpkin cupcakes have cooled, you can use a pastry gun, pastry bag, or knife to frost the cupcakes with the prepared vegan cream cheese frosting.

five gluten-free pumpkin cupcakes with vegan cream cheese frosting and extra cinnamon on top.

Recipe Tips & Tricks

  • Whisk the dry ingredients thoroughly so they look like one uniform mixture. The same goes for the wet ingredients. This allows you to then mix the dry and wet together easily without having to over-mix the batter.
  • Depending on how watery your pumpkin puree is, you may need more or less vegan milk, which is why it is added separately from the rest of the wet ingredients. If you need more liquid, add just more milk, not more vinegar.
  • The oil in the cupcakes helps prevent the cupcake from sticking to the liners; however, you can always spray the paper liners with non-stick spray. If you want to bake the cupcakes without liners, you MUST grease the cupcake tin extremely well to prevent sticking and allow for easy removal.
  • Don't frost warm cupcakes! Make sure the cupcakes are completely cooled; otherwise, the frosting will melt and slide off. I suggest cooling them overnight.
  • You can use whatever type of frosting you'd like, but I highly recommend vegan cream cheese frosting! I also like to add a sprinkle of cinnamon to the tops for extra pizzazz.

bitten into gluten-free pumpkin cupcake with cream cheese frosting on plate.

Storage & Freezing Instructions

  • Storage: Unfrosted baked pumpkin cupcakes can be stored at room temperature in a closed container for 2-3 days. Once you frost the cupcakes, using vegan cream cheese frosting, you'll need to store them in the fridge to prevent spoilage. Leftover frosted cupcakes are best if eaten within 1 week when stored in the fridge. Allow the cupcakes to sit out on the counter for a few minutes before serving for the best flavor.
  • Freezing: After allowing your baked gluten-free vegan pumpkin cupcakes to cool completely, you can freeze the unfrosted cupcakes by freezing them flat on a baking sheet until solid before transferring them to a Ziplock storage bag or container. If you want to freeze frosted cupcakes, freeze them in a single layer in a storage container to keep the frosting presentable. Thaw the cupcakes in a single layer at room temperature for a few hours before frosting the unfrosted or serving the pre-frosted. Use frozen cupcakes within 3-4 months for best quality.
  • Make-Ahead: When it comes to cakes and cupcakes, I like to make the cake/cupcake 1 day in advance so it has time to cool completely. The frosting can be prepped 2-3 days in advance, and then it will be ready to use when you're ready to frost the cupcakes.

two rows of cream cheese frosted gluten-free pumpkin cupcakes.

More Gluten-Free Vegan Cupcake Recipes:

  • Chocolate Cupcakes
  • Vanilla Cupcakes
  • Coconut Cupcakes
  • Funfetti Cupcakes
  • Mint Chocolate Cupcakes
  • Red Velvet Cupcakes
  • Carrot Cake Cupcakes

serving plate with gluten-free vegan pumpkin cupcakes with cream cheese frosting and cinnamon.

Print

Gluten-Free Pumpkin Cupcakes (Vegan)

gluten-free pumpkin cupcakes with vegan cream cheese frosting on plate.
Print Recipe

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5 from 1 review

The best Gluten-Free Pumpkin Cupcakes are vegan, allergy-free, and so easy to make! Made with real pumpkin and cozy spices, these moist and fluffy eggless pumpkin cupcakes are topped with a sweet and tangy dairy-free cream cheese frosting! Baked in 20 minutes with simple ingredients, everyone will love this homemade recipe!

  • Author: Rebecca Pytell
  • Prep Time: 5 Minutes
  • Cook Time: 20 Minutes
  • Total Time: 25 minutes
  • Yield: 12 Cupcakes 1x
  • Category: Dessert
  • Method: Bake
  • Cuisine: American

Ingredients

Scale

Pumpkin Cupcake Batter:

  • 1 ¾ Cup Gluten-Free All-Purpose Flour
  • 1 TB Cornstarch or Arrowroot Starch
  • ½ Cup Granulated Sugar (or preferred granulated sweetener)
  • ½ Cup Dark Brown Sugar (or preferred brown sugar sweetener)
  • 1 ½ Tsp Baking Powder
  • ½ Tsp Baking Soda
  • 1 Tsp Pumpkin Pie Spice
  • ½ Tsp Cinnamon
  • ¼ Tsp Salt
  • 1 ½ Cups Pure Pumpkin Puree
  • ¼ Cup Neutral Oil
  • 3 TB Unsweetened Non-Dairy Milk
  • 1 TB White Vinegar
  • 1 Tsp Pure Madagascar Bourbon Vanilla Extract

Vegan Cream Cheese Frosting:

  • 8 oz Plain Vegan Cream Cheese (softened)
  • 1 Stick Vegan Butter (softened)
  • 3 Cups Powdered Sugar (or sugar-free powdered sweetener)
  • 1 Tsp Water or Unsweetened Non-Dairy Milk
  • ½ Tsp Pure Madagascar Bourbon Vanilla Extract

Instructions

  1. Preheat the oven to 350°F.
  2. In a large mixing bowl, whisk together the gluten-free flour, starch, granulated sugar, brown sugar, baking powder, baking soda, spices, and salt.
  3. In a small bowl, mix together the pumpkin, oil, vinegar, and vanilla until smooth, before adding it to the bowl of dry ingredients.
  4. Mix the wet and dry ingredients together until you have a thick, lumpy batter, before adding the vegan milk and giving the batter one last mix so it's smooth with no visible lumps.
  5. Line a standard 12-count cupcake pan with liners and add about 3 heaping tablespoons of the cupcake batter to each (about ¾ full).
  6. Bake in the oven for 20 minutes, until the tops are golden brown and a toothpick inserted into the middle comes out mostly clean.
  7. Allow the cupcakes to cool for about 5 minutes in the pan before transferring them to a wire rack to cool completely before frosting.

To Make The Frosting:

  1. Soften the vegan cream cheese and stick of vegan butter slightly before adding them to a stand mixer or large bowl with a hand mixer.
  2. Add the powdered sugar, vanilla, and water. Beat the mixture together until you get a thick and smooth frosting. Add more water if needed.
  3. Store the frosting in the fridge until ready to frost the cooled cupcakes.
  4. Add the finished frosting to a pastry gun, pastry bag, or use a knife to frost the cooled cupcakes to your liking.
  5. Sprinkle the tops of the frosted cupcakes with extra cinnamon, if desired.

Notes

  • Storage: You can bake your cupcakes ahead of time and store them unfrosted at room temperature in a closed container for 2-3 days. Once you frost the cupcakes, they must be stored in the fridge to prevent spoilage. Leftover frosted cupcakes are best if eaten within 1 week.
  • Freezing: You can freeze unfrosted cupcakes by freezing them flat on a baking sheet until solid before transferring them to a Ziplock storage bag or container. If you want to freeze frosted cupcakes, freeze them in a single layer in a storage container to keep the frosting presentable. Thaw the cupcakes in a single layer at room temperature for a few hours before frosting the unfrosted or serving the pre-frosted. Use frozen cupcakes within 3-4 months for best quality.
  • Make-Ahead: You can make the cupcakes 1-2 days in advance. The frosting can be prepped 2-3 days in advance, and then it will be ready to use when you're ready to frost the cupcakes.
  • If you don't have a pastry bag, you can use a Ziplock/plastic baggie. Simply fill the bag with frosting, snip one corner off, and squeeze the frosting onto the cupcakes.
  • Check out this recipe for vegan vanilla buttercream frosting if you don't want cream cheese frosting. If you want to use store-bought vegan cream cheese frosting, I recommend Miss Jones brand, which is also allergy-free. You can also use my vegan chocolate buttercream frosting recipe!

Nutrition

  • Serving Size: 1 Cupcake

Did you make this recipe?

Tag @rebeccagf666 on Instagram and hashtag it #strengthandsunshine

When it's the fall season, everything that can be pumpkin WILL be pumpkin, and that includes these delicious gluten-free pumpkin cupcakes!

So tell me:

+ What's your favorite pumpkin baked good?

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Stuffed Baked Apples (Gluten-Free, Vegan) »

Reader Interactions

Comments

  1. Beverly

    October 01, 2025 at 9:05 pm

    These cupcakes are fantastic! We loved them!

    Reply
    • Rebecca Pytell

      October 02, 2025 at 7:02 am

      That's great to hear!

      Reply
  2. Lisa

    September 28, 2025 at 6:13 am

    I am always on the lookout for good gluten free recipes. These look great!

    Reply
    • Rebecca Pytell

      September 28, 2025 at 5:32 pm

      Enjoy

      Reply
  3. Mariama

    September 26, 2025 at 6:52 am

    Pinned! It looks really yummy!

    Reply
    • Rebecca Pytell

      September 26, 2025 at 8:19 am

      Hope you enjoy them!

      Reply

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