Gluten Free Pumpkin Cupcakes For Two
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Small batch pumpkin cupcakes that are 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.

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 classic pumpkin cupcake recipe.
While I have an assortment of pumpkin small batch 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 small batch whoopie pies, and their counterpart gluten free small batch pumpkin whoopie pies.
Tasty Details
- Moist – The cupcakes are incredibly moist with a fluffy and light sponge. Thanks to a thoughtfully tested blend of gluten free flours.
- Full of Flavor – These cupcakes are brimming with pumpkin flavor.
- Spicy – Pumpkin spicy that is. All the cozy flavors of cinnamon, nutmeg, ginger, and clove, and I do not skimp on the spice!
- 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!

Helpful Tips
- 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.
- 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.

Recipe FAQ
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.
Yes. As long as you read the label and the only ingredient is pumpkin. Different brands choose different names.
The cupcakes can be stored covered at room temperature.


Gluten Free Pumpkin Cupcakes
by Erin Cernich
Equipment
Ingredients
- 5 tablespoons blanched almond flour
- 2 ½ tablespoons arrowroot flour
- 1 ½ tablespoons coconut flour
- 1 tablespoon sweet white rice flour
- ¼ teaspoon baking powder
- ⅛ teaspoon baking soda
- ⅛ teaspoon salt
- 1 teaspoon pumpkin pie spice
- 2 tablespoons coconut oil, melted
- ¼ cup granulated sugar
- 2 tablespoon pure maple syrup
- 1 large egg, room temperature
- 2 tablespoons milk, any kind (room temperature)
- ¼ teaspoon apple cider vinegar (or white distilled vinegar)
- ¾ teaspoon vanilla extract
- ¼ cup pure canned pumpkin
- Whipped Chocolate Ganache
Instructions
- 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 white 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 coconut oil, melted, ¼ cup granulated sugar, 2 tablespoon pure maple syrup, 1 large egg, room temperature, 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. Tip – Use 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 small batch frosting of choice.
Notes
- 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 small batch 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.
Nutrition Estimates
TRY THESE SMALL BATCH RECIPES NEXT!

About the Author …
Hi, I’m Erin! With years of experience baking for two in my own small household, I know about the love for desserts without the leftovers. I’ve tested, written, and photographed every one of the 300+ recipes on my website. And even had some of my desserts featured on Taste of Home, The Spruce Eats, ELLE, Parade, and more! From traditional to gluten free desserts for two, I have the recipe for you.
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