Gluten Free Pumpkin Cupcakes

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This small batch recipe for pumpkin cupcakes is gluten free and bursting with fall flavors!  The cupcakes are moist, delicately sweet, and made with an almond flour blend, pumpkin pie spice, and pure pumpkin puree.  Frost the cupcakes with whipped chocolate ganache frosting for a deliciously festive fall cupcake.

A single gluten free pumpkin cupcake with chocolate frosting on a fall plate.

Gluten Free Pumpkin Cupcakes

You know it is officially fall when a pumpkin cupcake recipe hits the blog!  And I’m pumped about this particular pumpkin cupcake recipe.  Not only because I was able to dust off my jar of pumpkin pie spice, but I have a gluten free counterpart to my original classic pumpkin cupcake recipe

While I have an assortment of pumpkin recipes, I’ve been having a lot of fun taking some of the original recipes on and making them gluten free.  Like the classic pumpkin whoopie pies, and their counterpart gluten free pumpkin whoopie pies.

A Tasty Summary Of These Cupcakes

  1. Gluten Free – Much like the majority of my gluten free recipes, these are made with an almond flour blend:  almond flour, arrowroot flour, coconut flour, and sweet rice flour.
  2. Small Batch – This recipe makes 5 cupcakes.  That could also be made into a single layer 6-inch cake.
  3. Moist – Often with gluten free desserts you may think dry and flavorless.  That is not these cupcakes.  They are incredibly moist with a fluffy and light sponge.  Thanks to a thoughtfully tested blend of gluten free flours.   
  4. Full of Flavor – These gluten free cupcakes are brimming with sweet cupcake and pumpkin flavor.  I will go so far to say, it is hard to tell they are gluten free!
  5. Spicy – Pumpkin spicy that is.  All the cozy flavors of cinnamon, nutmeg, ginger, and clove, and I do not skimp on the spice!  And if it is fall spice you crave, also check out the gluten free spice cupcakes and gluten free apple spice cupcakes!
  6. Easy – I used a couple of bowls and a fork to make these cupcakes.  So no need to break out the fancy equipment or tools!
Three pumpkin gluten free cupcakes with chocolate frosting lined up in a row on a table.

What You’ll Need To Make A Small Batch of Gluten Free Pumpkin Cupcakes

dry Ingredients

  • Almond Flour – Super fined, blanched almond flour.  I’ve provided a (affiliate) link in the recipe.  Almond flour is moist, has binding properties, makes cakes light, has a pleasant sweet flavor.
  • Arrowroot Flour – Also called arrowroot starch.  They are the same thing.  Arrowroot assist with structure and the soft texture of the cupcakes.
  • Coconut Flour – Coconut flour has absorbency properties that work well with moisture rich ingredients – like canned pumpkin.
  • Sweet Rice Flour – I like sweet rice flour for the soft texture it provides while also providing binding properties.  Great when you are baking without gluten!
  • Baking Powder and Baking Soda – We use both for texture and lift.  Gluten free baking often benefits with a little extra leavener.
  • Salt – Flavor balancer and enhancer.
  • Pumpkin Pie Spice – You can certainly make your own blend, but I often reach for the store-bought!

Wet Ingredients

  • Pumpkin – Canned, pure, pumpkin.  Not pumpkin pie filling.
  • Coconut Oil – Cold pressed refined coconut oil, that is melted.  Cold pressed coconut oil has had moisture removed, leaving it in a solid form.
  • Cane Sugar – The sugar adds (obvious) sweetness.  However, for these pumpkin cupcakes, it is also key in the texture.  Gluten free bakes can get dense very quickly.  And this is especially so with moisture rich ingredients (specifically pumpkin).  The cane sugar helps to keep the cupcakes soft.  I choose organic cane sugar because it is not as refined as regular table sugar.
  • Pure Maple Syrup – A little for a different sweet flavor.  And make sure it is pure maple syrup, and not pancake syrup!
  • Milk – Any milk will work.  I use unsweetened SoDelicious coconut milk.
  • Egg – 1 large egg is all we need!
  • Apple Cider Vinegar – The vinegar works with the baking soda for that extra lift in the cupcakes.
  • Vanilla – Flavor!

Baking Equipment

  • Cupcake Pan
  • Mixing Bowls

Frosting flavors For Fall Cupcakes

We’ve gone over what you need to make the Gluten Free Pumpkin Cupcakes, but what about a frosting for them?!  All of the photos highlight the chocolate ganache frosting.  Because pumpkin and chocolate are a tasty combination.  I got the idea from my pumpkin roll cake with chocolate filling recipe!

However, I find pumpkin to be a pretty versatile flavor, and you could pair it with almost any flavor:  

See, the flavor possibilities are tasty and vast!

Tips For Success When Making Gluten Free Cupcakes

  • Use room temperature ingredients – This is applicable for the pumpkin (if you have it refrigerated), milk, and egg.  When ingredients are all at the same temp, they will mix and bake more evenly.
  • Let the cupcake batter rest before baking – I like to let this particular gluten free batter rest because of the sweet rice flour.  This gives the batter time to hydrate, which I find the rice flour needs.  
  • Use a cookie scoop to portion the batter – I love my medium size cookie scoop!  It’s my go-to for most of my cookie recipes, but I also reach for it when I need to portion batter equally.
  • Bake the full time – Gluten free baked goods need longer to bake all the way through.  They can be deceiving though.   The touch test and toothpick test may tell you they are done minutes earlier.  However, keep the cupcakes in the oven the full time noted.  Otherwise, you can end up with dense cupcakes.
  • Cool the cupcakes completely – For two reasons:  frosting warm cupcakes is generally a bad idea, and gluten free baked goods taste better when they are completely cool.  This is my opinion, but I’ve yet to eat a warm gluten free anything and have it taste as good as when it has time to cool.
  • Try without substitutions – At least the first time.  Gluten free baking can be even more tricky than traditional baking.  Each gluten free flour works differently and most often they need to be blended to get the best results.
A gluten free pumpkin cupcake with chocolate frosting cut in half and placed on a small cupcake stand.

faq’s: small batch gluten free pumpkin cupcakes

Can I double the recipe?

I have only tested a small batch and cannot say how doubling the recipe will turn out. It you try it, let me know!

Will a 1:1 gluten free flour work instead of the almond flour blend?

Probably not. My flour blend and the flours in the 1:1 blends are different, thus have different baking characteristics. Other ingredients would likely need to be adjusted, and I have not tested with a 1:1 to say what those would be.

Can I substitute regular sugar for the organic cane sugar?

You should be able to without affecting the result. I prefer organic cane sugar because it is not as refined as white table sugar.

Is canned pumpkin, pure pumpkin, and pumpkin puree the same thing?

Yes. As long as you read the label and the only ingredient is pumpkin. Different brands choose different names.

How do I store leftover cupcakes?

The cupcakes can be stored covered at room temperature.

A frosted gluten free pumpkin cupcake set on a wooden plate with the cupcake liner removed.
A single gluten free pumpkin cupcake with chocolate frosting on a fall plate.
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5 from 2 reviews

Gluten Free Pumpkin Cupcakes

Yield: 5 Cupcakes
This small batch recipe for pumpkin cupcakes is gluten free and bursting with fall flavors!  The cupcakes are moist, delicately sweet, and made with an almond flour blend, pumpkin pie spice, and pure pumpkin puree.  Frost the cupcakes with whipped chocolate ganache frosting for a deliciously festive fall cupcake.
Prep15 minutes
Cook27 minutes
Total42 minutes


  • 1 – Muffin/Cupcake Pan



  • Preheat the oven to 325F degrees and adjust the oven rack to the middle position. Place 5 cupcake liners in the cupcake pan.
  • In a small mixing bowl, whisk together the almond flour, arrowroot flour, coconut flour, sweet rice flour, baking powder and soda, salt, and pumpkin pie spice.
    5 tablespoons blanched almond flour, 2 ½ tablespoons arrowroot flour, 1 ½ tablespoons coconut flour, 1 tablespoon sweet rice flour, ¼ teaspoon baking powder, ⅛ teaspoon baking soda, ⅛ teaspoon salt, 1 teaspoon pumpkin pie spice
  • In a medium mixing bowl, add the oil, sugar, and maple syrup. Stir to combine. Add the egg, milk, vinegar, vanilla, and pumpkin. Stir until completely combined and smooth.
    2 tablespoons cold pressed refined coconut oil, melted, ¼ cup organic cane sugar, 2 tablespoon pure maple syrup, 1 large egg, 2 tablespoons milk, any kind, ¼ teaspoon apple cider vinegar, ¾ teaspoon vanilla extract, ¼ cup pure canned pumpkin
  • Sprinkle the dry ingredients over the wet and stir the batter until no dry streaks remain. Equally portion the batter into the cupcake liners and let the batter rest for at least 5 minutes. This allows the batter to hydrate. TipUse a cookie scoop to portion the batter into equal amounts, and less mess!
  • Bake the cupcakes for 25 to 27 minutes, or until they are springy to the touch and a toothpick inserted in the middle comes out clean. Cool the cupcakes in the pan set on a wire cooling rack for 10 minutes, then transfer the cupcakes to rack to cool completely.
  • Allow the cupcakes to cool completely before frosting. Frost with the Whipped Chocolate Ganache Frosting (pictured), or any frosting of choice. Enjoy!
    Whipped Chocolate Ganache Frosting
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  • Serving Size – I have tested this recipe many times and 5 cupcakes yields the most optimal results.  You don’t want to overfill the cupcake liners, and trying to get all of the batter into 4 cupcakes will result in cupcakes that are not baked properly.
  • Pumpkin – Be sure to use canned pumpkin and not pumpkin pie filling.
  • Leftover Pumpkin – You will have leftover pumpkin, regardless of the size can you use.  Check out my other pumpkin recipes to make another batch of pumpkin treats!
  • Substitutions – I have only tested this recipe with the ingredients listed.
  • Cake – This recipe can also work to make a single layer 6-inch cake.  Keep an eye on the bake time, as the cake may take a few minutes longer to bake.
  • Vinegar, Baking Powder, and Baking Soda – I use all 3 ingredients to get the desired lift and texture of a cupcake.  Gluten free bakes tend to need a little more help to rise.
  • Rest the Batter – I recommend a few minute rest time before baking to allow the batter to hydrate.  I find this especially helpful when baking with sweet rice flour.
Course: Dessert
Cuisine: American
Author: Erin Cernich
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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