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Gluten Free Chocolate Cupcakes

I am planning to make a cake for my friend’s wedding this spring, and she can’t eat gluten. This is the catalyst behind my recent gluten free baking spree, and these gluten free chocolate cupcakes.

Gluten free baking is different than conventional baking in a lot of ways, and really throws the rule book out when it comes to baking. It’s a totally different animal, which has taken a lot of trial and error for me to get comfortable with.

image of gluten free chocolate cupcakes frosted with a dark chocolate buttercream frosting

What’s In Gluten Free Flour??

There are a lot gluten free flour blends out there. Each brand uses a unique mixture of wheat flour alternatives, like rice flour, brown rice flour, and even almond flour!

It can be difficult to get the texture of gluten free flour just right for baking. A lot of these alternative flours have a finer texture than all-purpose flour.

Some type of starch is usually added to help give the mixture better structure, and a bit of binding power. Tapioca and potato starch are the most commonly used starches.

image of ingredients for gluten free chocolate cupcake reipe

One other ingredient in gluten free flour that might sound a little strange is xanthan gum. It’s a key ingredient in gluten free baking. Xanthan gum has a big impact on the texture of gluten free baked goods too.

Gluten adds an elasticity and stickiness to dough and batter. Xanthan gum emulates these characteristics in gluten free baking, and helps lock in moisture.

Does It Matter What Brand of Gluten Free Flour I Use?

I’ve tried this recipe with a few different brands of gluten free flour, and so far each of them has worked great:

My favorite brand of gluten free flour for this recipe was King Arthur. However, any brand of gluten free flour you can find at your grocery store should work.

image of gluten free chocolate cupcake unwrapped to show how moist and fluffy the cupcakes are

My only word of caution is to be sure you use some sort of gluten free flour blend.

Using a single type of gluten free flour like almond flour or cassava flour in this recipe will not yield the same results!

Most grocery stores carry at least one blend of gluten free flour. Stores like Whole Foods or Trader Joe’s also have lots of great options.

If all else fails, amazon is another easy way to get your hands on a gluten free flour blend. I order a majority of my baking supplies on amazon, including most of my specialty ingredients ?

Why This Recipe Works With Gluten Free Flour

This gluten free chocolate cupcake recipe is based on my moist chocolate cupcake recipe.

Gluten free baked goods have come a long way in the past few years, but a lot of people still think of them as gritty, dense, and even gummy.

One of the main reasons this cupcake recipe works is because it uses oil as a fat instead of butter. Oil is easier for the gluten free flour to absorb.

image of gluten free cupcakes in the baking pan, surrounded by ingredients and frosting

The cupcake texture was spot on, with the help of the following gluten free baking tips.

Tip #1: Overmix Your Batter

While I strongly advise against over mixing batter in other recipes, and even design my recipes to have as little mixing as possible, gluten free batter is different.

The whole reason you don’t want to over mix your batter is that it develops thick strands of gluten, which can lead to dense, tough cupcakes. But when you’re using gluten free flour, this isn’t a problem.

In fact, overmixing gluten free flour can actually give the cupcake better structure! This helps cupcakes rise better as they bake, and gives the cake a more tender crumb.

image of gluten free chocolate cupcake cut in half to show great structure and delicate crumb

The additional mixing can also make it easier to bite into these cupcakes and enjoy them. The incremental structure helps prevent the cupcakes from crumbling as they’re bitten into.

Tip #2 Let Your Batter Rest

Remember earlier when I said that gluten free flour blends can have a hard time absorbing moisture and fats?

If you let the batter sit for a bit before baking it, you give the flour more time to absorb all that goodness. This helps thicken the batter, and prevents your cupcakes from having a gritty texture.

I unintentionally did this as I was photographing and filming this gluten free chocolate cupcake batter. You’d be surprised how long it takes to get a perfect shot of scooping cupcake batter into a pan!

Letting the batter sit for about 30 minutes drastically improves the texture of these cupcakes, so be sure you don’t skip this step!!

image of baked chocolate gluten free cupcakes stacked in a pile, ready to be frosted

Tips for Making The Best Gluten Free Chocolate Cupcakes:

  • Don’t be afraid to overmix your batter! Vigorously whisk your batter for a few minutes once it’s made, to help give it structure
  • Let your batter sit for about 30 minutes before baking to help the gluten free flour absorb more moisture from the batter
  • Properly measure your gluten free flour (spoon into the cup measure then level) or use a kitchen scale to measure your dry ingredients
  • Use a cookie scoop to easily fill your cupcake liners
  • Ingredients at room temp mix together better, so be sure you set out any cold ingredients ahead of time.
  • Bang your cupcake pan on the counter before putting it in the oven, to bring any air bubbles that are trapped in the batter to the surface

Making These Cupcakes Cake In Advance & Storage Tips:

  • Make your cupcakes in advance! If stored unfrosted in an airtight container, they can last for 2 days at room temp, up to a week in the fridge, or up to 3 months in the freezer
  • Make your frosting ahead of time too, or save any leftover frosting! It can be stored in an airtight container in the fridge for up to a month, or in the freezer for up to 3 months. Be sure to give it a good stir once it thaws to get the consistency nice and smooth again.
  • Frosted cupcakes can sit out at room temperature overnight in an airtight container, but I find frosting them right before serving is best.
image of gluten free chocolate cupcakes frosted with a swirl of dark chocolate frosting

Let Me Know What You Think!

If you try this recipe for gluten free chocolate cupcakes, I’d love to hear what think of it! Please leave a rating, and let me know your thoughts in the comments section.

Other Gluten Free Recipes You Might Like:

Yield: 12

Gluten Free Chocolate Cupcakes

image of gluten free chocolate cupcakes frosted with a dark chocolate buttercream frosting

This recipe for gluten free chocolate cupcakes is incredibly moist and fluffy, and is fool-proof using two simple gluten free baking tips!!

Prep Time 10 minutes
Cook Time 18 minutes
Additional Time 45 minutes
Total Time 1 hour 13 minutes


Gluten Free Chocolate Cupcake Batter

  • 3/4 cup hot water (177 grams)
  • 1/3 cup milk or dark chocolate chips, melted (57 grams)
  • 1 tsp instant espresso or coffee (2 grams)
  • 1/3 cup baking cocoa powder (32 grams)
  • 3/4 cup gluten free flour (92 grams)
  • 3/4 cup granulated sugar (150 grams)
  • 1/2 tsp salt (2 grams)
  • 1/2 tsp baking soda (3 grams)
  • 1/3 cup vegetable oil (73 grams)
  • 2 large eggs, room temperature (114 grams)
  • 1 tsp white vinegar (4 grams)
  • 1 tsp vanilla extract (4 grams)

Chocolate Buttercream Frosting

  • 1/2 cup (or 1 stick) unsalted butter, room temperature (113 grams)
  • 1 1/2 cups powdered sugar (188 grams)
  • 1/2 cup melted dark chocolate, cooled (90 grams, 4 oz.)
  • 1/4 tsp salt (2 grams)
  • 1/2 tsp vanilla extract (2 grams)
  • 1/4 cup heavy cream (60 grams)


Chocolate Cupcake Recipe:

  1. Begin by preheating oven to 350°F (175°C), and place 12 cupcake liners in cupcake pan.
  2. Add 3/4 cup of (VERY) hot water into a large bowl.
  3. Carefully pour in 1/3 cup melted chocolate chips, 1 tsp instant espresso powder, and 1/3 cup sifted cocoa powder.
  4. Whisk together until the ingredients have combined.
  5. Sift the dry ingredients into the wet ingredients (3/4 cup gluten free flour, 3/4 cup granulated sugar, 1/2 tsp salt and 1/2 tsp baking soda) into chocolate espresso mixture, and stir until combined.
  6. Scrape the sides and bottom of the bowl as needed with a spatula.
  7. Add 2 large eggs, 1/3 cup vegetable oil, 1 tsp vinegar, and 1 tsp vanilla, and mix until the batter is smooth.
  8. Mix the batter for an additional 2 minutes, to help give the batter structure. You don't have to worry about overmixing, because there's no gluten in this batter!
  9. Cover and let the batter sit for about 30 minutes, to give the gluten free flour tiem to absorb more of the liquid in the batter.
  10. Fill cupcake liners 3/4 full, and bake for about 18-19 minutes, or until a toothpick comes out clean.
  11. Allow the cupcakes to cool for 5 minutes before moving them to a cooling rack to finish cooling.

Chocolate Buttercream:

  1. Beat the butter on a medium speed for 30 seconds with a paddle attachment, until smooth. 
  2. Mix in the vanilla extract and salt on a low speed.
  3. Slowly add in the powdered sugar in two installments. Alternate with the heavy cream.
  4. Mix in the cooled, melted chocolate.
  5. Beat on low until the ingredients are fully incorporated, and the desired consistency is reached.
  6. If the frosting is too thick, add an extra Tbsp of heavy cream. If it's too thin, add in another 1/2 cup of powdered sugar.
  7. Stir by hand with a rubber spatula to get the frosting SUPER smooth.
  8. Place in a piping bag fitted with an Ateco 869 tip, and pipe a swirl on top of each cupcake.


This recipe can also be used to make mini cupcakes! This recipe makes about 40 mini cupcakes, which only need to bake for 9-10 minutes.

These cupcake can be made in advance! If stored unfrosted in an airtight container, they can last for:

  • 2 days at room temp
  • Up to a week in the fridge
  • Up to 3 months in the freezer

If you have extra buttercream you don't use, it can be stored in the fridge in an airtight container or piping bag for up to 2 weeks.

Nutrition Information



Serving Size


Amount Per Serving Calories 417Total Fat 18gSaturated Fat 7gTrans Fat 0gUnsaturated Fat 9gCholesterol 43mgSodium 230mgCarbohydrates 62gFiber 2gSugar 50gProtein 4g

Lisa Schaaf

Tuesday 21st of May 2024

Can this cupcake recipe be doubled? My apologies if you already have this message. I wasn’t sure it sent. Thank you

Lisa Schaaf

Tuesday 21st of May 2024

Can this recipe be doubled?


Saturday 13th of April 2024

Hi! I cannot find any UNSWEETENED applesauce where I live. Can I use sweetened applesauce in place of eggs? Thanks!


Monday 22nd of April 2024

Hi Sana,

Great question! You can totally use sweetened applesauce if you can't find unsweetened applesauce. Hope that helps, happy baking!


Saturday 13th of April 2024

Hi! I absolutely adore this recipe you can’t even tell it’s gluten free! I have a question and I was wondering if you could help.

I follow the instructions exactly but every time a good few of my cupcakes get a spot where they decide to puff up and sometimes go over the case.

Do you have any recommendations??


Saturday 13th of April 2024

Hi Aimee,

I'm so happy to hear that you love this recipe :) If the cupcakes are overflowing a tiny bit on the sides of your pan, I'd recommend filling them the tiniest bit less full! Cupcake pans and cupcake liners can vary a bit in size, and that can mean that sometimes they can be a bit over-filled even when you follow the recipe to a T. I'd say try to have a little bit of leftover batter (maybe a Tablespoon) and see if that helps, hopefully it does! Happy baking!!


Tuesday 26th of March 2024

Hey! If you’re flour blend doesn’t have xanthan gum in it already, how much do I add into the recipe? Thanks

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