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Looking for a classic gluten free cupcake recipe that everyone can enjoy? These Gluten Free Vanilla Cupcakes are moist with a simple sweet vanilla flavor. They’re also dairy-free and made without any refined sweeteners. Everyone is going to love them, and nobody will suspect they’re gluten-free!

Gluten free vanilla cupcakes.

Gluten Free Cupcake Recipe

In my opinion, a cupcake should be at least three things: moist, rich and not overly sweet. These gluten free Vanilla Cupcakes check all those boxes and more! These simple-to-make cupcakes are a bit on the healthier side because they are dairy-free, made primarily with almond flour (hello nutrients!) and contain no added refined sugars. Yet, they taste sinfully good.

And the bonus is you only need a few simple tools to mix them up! We have a few different options to frost them, including some dairy free options, in case you need them. So grab a bowl and a whisk and lets get baking!

Ingredients Needed for Gluten Free Cupcakes

Here is an overview of the GF vanilla cupcake ingredients. The full recipe is located at the end of this post.

  • Almond Flour
  • Coconut Flour
  • Baking Powder
  • Baking Soda
  • Sea Salt
  • Eggs
  • Honey
  • Apple Sauce
  • Vanilla
  • Butter
  • Powdered Sugar
  • Sprinkles (Optional)

Tools We Used

Here are the recommended tools needed to bake cupcakes!

Why This is the Best Gluten-Free Cupcake Recipe

Aside from the health benefits of using more nutrient dense naturally gluten-free flours in this cupcake, the combination of almond and coconut flour is so moist and tender in the final result!

We also love that this is a fool proof recipe since there is no concern about the cake being tough from over-beating the batter like there is with a gluten flour containing cupcakes. And it’s really simple to make.

Gluten free vanilla cupcakes on a cooling rack.

What Type of Frosting to Use

We’ve included a simple buttercream frosting recipe in the instructions below. However, it contains dairy. If you need a dairy-free frosting, check out:

Buttercream frosting.

A Note About Sprinkles

We stay away from artificially dyed sprinkles when we can. Lucky for us there are so many good brands out there for naturally dyed sprinkles derived from fruits, vegetables and herbs. If you are looking to get that classic cupcake look with some rainbow sprinkles, check out some naturally dyed options.

Here is a list of some of the ones we’ve tried and liked:

  • India Tree
  • ColorKitchen Foods
  • Let’s Do Organic: This one will add some color to the blondies but are similar to nonpareils. We’ve added this to the list because this brand can be purchased at a few natural grocery stores and Whole Foods and might be easier to find, though these would be our last choice.
Gluten-free vanilla cupcakes.

How to Store Them

These cupcakes will keep well in the refrigerator fully decorated for up to 3 days. If you wanted to bake the gluten-free cupcakes ahead of time, you could keep them in the refrigerator for up to 5 days, or freeze them for up to 3 months.

Looking for more gluten-free cake/cupcake recipes? Check out these others:

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Gluten-free vanilla cupcakes.

Gluten-Free Vanilla Cupcakes

5 from 1 vote
Looking for a classic vanilla cupcake recipe that everyone can enjoy? These Gluten Free Vanilla Cupcakes are moist with a simple sweet vanilla flavor. They’re also dairy-free and made without any refined sweeteners. Everyone is going to love them, and nobody will suspect they're gluten-free!
Servings 9 cupcakes
Prep Time 15 minutes
Cook Time 15 minutes


For Cupcakes:

  • 1 cup almond flour
  • 1 tablespoon coconut flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • Pinch of fine sea salt
  • 3 eggs
  • 3 tablespoons honey or pure maple syrup
  • 2 tablespoons unsweetened applesauce
  • 1 teaspoon vanilla extract

For Vanilla Buttercream:

  • 1 cup unsalted butter
  • 3 cups powdered sugar
  • 1 teaspoon vanilla extract
  • 1 tablespoons almond milk or nut-milk of choice more if needed


  • Preheat the oven to 350°F and line 9 muffin tins with parchment paper liners or silicone liners.
  • In a bowl, whisk together the almond flour, coconut flour, baking powder, baking soda, and salt until well blended.
  • Add the eggs, honey, applesauce, and vanilla extract and mix until smooth.
  • Pour into the lined muffin cups, filling each about 1/2 full, and bake for 15 to 20 minutes, or until a toothpick inserted in the middle comes out clean.
  • Transfer cupcakes to cooling rack. While cupcakes cool, make the frosting: In a stand mixer fitted with a whisk attachment or using a hand mixer, mix the butter for 1 minute. Add the powdered sugar and mix on low speed until well blended, then increase the speed to medium and beat until fluffy, about another 3 to 5 minutes. Add the vanilla, and almond milk. Continue to beat on medium speed for 1 minute, adding an additional tablespoon of almond milk, or more, if needed for a soft consistency.
  • Apply the frosting in a mound on the cupcake with a spatula or using a piping bag fitted with a circle piping tip.
  • Add sprinkles to the top of the buttercream.


Cupcakes will keep in the refrigerator for up to 3 days.


Serving: 1cupcakeCalories: 65kcalCarbohydrates: 6gProtein: 3gFat: 3gSaturated Fat: 1gCholesterol: 62mgSodium: 153mgFiber: 1gSugar: 4g
Keyword: Gluten-free Vanilla Cupcakes
Course: Sweets
Method: Bake
Author: Lexi's Clean Kitchen

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  1. RE: Gluten free vanilla cupcakes

    The calories listed for each one of these 9 cupcakes is “65kcal.” Is each one of these only 65 calories, or was this a typo?


  2. 5 stars
    thank you for these cupcakes, especially for balancing all of the alternative ingredients, I never know how much of each ingredient like almond flour to use, much appreciated!