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Gluten Free Chocolate Cupcakes

Decadent and rich gluten free chocolate cupcakes are loaded with cocoa powder and bake up unbelievably moist and tender. Top them with a fluffy chocolate buttercream or your favorite frosting recipe. Plus, they need just one gluten free flour – whole grain oat flour – to make!

A cake stand holds gluten free chocolate cupcakes.

Easy Gluten Free Chocolate Cupcakes Recipe

Soft, squidgy, and utterly irresistible, gluten free chocolate cupcakes are one of my favorite things! You seriously won’t believe these cupcakes are gluten-free – they taste exactly like “regular” cupcakes but they’re made with superstar oat flour with no other gluten free flours needed. These cupcakes have been taste-tested on kids and adults alike and always receive rave reviews. And, this recipe makes a lot, two dozen cupcakes to be exact, making it a great choice for birthdays, picnics, you name it. Frost these beauties with your favorite frosting, be it chocolate, cream cheese, Swiss buttercream, or a drizzle of caramel sauce – you do you!

Why You’ll Love Them!

  • One gluten free flour: Versatile and always-reliable, gluten free oat flour creates a sturdy, moist cupcake that holds up well to all sorts of decadent toppings.
  • So easy! Two bowls and a whisk are all you need to whip these cupcakes up.
  • Amazing texture: Oat flour performs so beautifully in almost any recipe you can think of, soaking up the liquid in the batter to create a gorgeously tender cupcake that’s never dry or crumbly.
The ingredients for gluten free chocolate cupcakes are shown: cocoa powder, sugar, brown sugar, baking powder, baking soda, salt, coffee, eggs, greek yogurt, milk, vanilla.

Ingredients You’ll Need

Here’s the list of ingredients for these gluten free chocolate cupcakes. The full ingredient amounts are in the recipe card lower down – this is just an overview.


  • Oat flour – Wonderful for baking, gluten free oat flour in this recipe creates an imperceptibly gluten-free chocolate cupcake. Grab a bag or easily make your own oat flour.
  • Brown sugar – Light or dark brown sugar works interchangeably in this recipe.
  • Granulated sugar – A bit of granulated sugar alongside the brown sugar brings sweetness.
  • Cocoa powder – Use unsweetened cocoa powder so it doesn’t overpower the cupcakes.
  • Leavening – Baking soda and baking powder help the cupcakes to rise.
  • Salt – I always use fine sea salt in my recipes!
  • Coconut oil – You’ll use melted coconut oil – either unrefined or refined coconut oil works fine. You could also use vegetable oil or olive oil.
  • Eggs – Large eggs hold the batter together.
  • Greek yogurt – You can use non-fat, low-fat, or full-fat Greek yogurt.
  • Milk I use whole milk for richness; 2% milk works, too.
  • Pure vanilla extract
  • Coffee – You can save a bit of coffee from your morning pot, or use instant coffee. If you don’t drink coffee, go ahead and use hot water.


  • Butter – Always use unsalted butter.
  • Semisweet chocolate
  • Powdered sugar
  • Milk
Three gluten free chocolate cupcakes on a decorative plate.

How to Make Gluten Free Chocolate Cupcakes

I’ve outlined the steps you’ll need to take to make these luscious cupcakes below. The detailed instructions are in the recipe card.

  • Prep: Line two cupcake tins with liners.
  • Whisk dry: Whisk together the oat flour, sugars, cocoa powder, baking soda, baking powder, and salt.
  • Combine wet: Whisk together the coconut oil, eggs, yogurt, milk, and vanilla.
  • Combine: Stir the dry ingredients into the wet ingredients.
  • Add coffee: Stir in the coffee.
  • Place in tins: Divide the batter evenly between the cups and preheat the oven to 350°F.
  • Bake: Place pans in the oven and bake until a toothpick in the center comes out clean.
  • Cool: Remove from oven and let cupcakes cool in the pans then turn out onto a rack to cool fully.
  • Frost: Frost the cupcakes with your favorite frosting.
A top down shot of chocolate frosting on top of a gluten free chocolate cupcake.

Recipe Tips & Tricks

Check out a few of my tips to makes these cupcakes turn out perfectly:

  • Rest the batter: Let the batter rest for a bit before baking. Oat flour, like all gluten free flours, benefits from a rest to let it absorb liquids. I find that resting the batter in the tins while the oven preheats is just enough time for the oat flour to hydrate. I’ve included this step in the recipe directions.
  • Substitute hot water: If you don’t drink coffee, you can substitute 1 cup of hot water for the coffee if needed. Or, you can use (decaffeinated if needed) instant coffee or instant espresso if you don’t regularly brew coffee at home.
  • Use room temperature ingredients: Whether you’re making a regular cake or a gluten free cake, bringing the ingredients to room temperature is important! It helps them to better incorporate into the batter, making for a better-structured cake after it’s baked.
  • Cool the cake completely: Oat flour cupcakes can be softer than wheat flour cupcakes, especially when they’re warm (although, every baked item needs to cool a bit regardless of whether it’s gluten free). Make sure to cool the cupcakes thoroughly before frosting them.
  • Save some coffee: I’ll often plan ahead when I’m making my morning pot of coffee and brew a little bit extra to use in the cake so it’s ready to go when I put the batter together (a quick blast in the microwave or heat on the stove will warm it up nicely). Or, if I have a cup or so of coffee left over, I’ll place it in a jar and keep it in the fridge until I’m ready to make this recipe.
  • Make ahead: You can bake the cupcakes up to 24 hours in advance and I recommend doing this! Most cakes benefit from resting in the fridge overnight so their flavor deepens and the crumb firms up a bit. This will also make it easier to frost the cupcakes. Store the cupcakes, either unfrosted or frosted, covered with foil, or in an airtight container in the fridge.
  • Frosting tip: Sift the powdered sugar before adding it to the buttercream. This is SO important to eliminate any clumps in the frosting.
  • Any kind of frosting: I’ve included a simple recipe for my favorite frosting – chocolate buttercream. But, you can use any frosting you like to finish these cupcakes! Try vanilla buttercream, meringue, cream cheese frosting, or even whipped cream …
  • Halve the recipe: This recipe makes enough for 2 dozen cupcakes. That’s a lot! If you don’t want 24 cupcakes, you can go ahead and cut the recipe in half to make 12 cupcakes.
  • Make it dairy-free: Choose your favorite non-dairy milk and non-dairy yogurt to use in the batter.
  • Make it refined sugar-free: Substitute coconut sugar for the brown sugar and granulated sugar.
  • Make it egg-free: I haven’t tried making this as a vegan or egg-free chocolate cake, but you could experiment with using a flax egg substitute in place of the eggs. Oat flour does need some kind of a binder – eggs work perfectly – but you might have success using flax eggs.

Why Use Oat Flour?

Oat flour is my favorite gluten-free flour to use in baking recipes. In many recipes, you can do a straight 1:1 swap if you measure the flour by weight (I’ve included both weight and cup measurements to keep things easy for you in the recipe card.) In this gluten free chocolate cupcakes recipe, the cupcakes bake up beautifully and don’t have the denseness or grittiness you may find in baked goods that rely on a gluten-free all-purpose flour substitute. If you need to substitute for oat flour, try sorghum flour or teff flour, another gluten free flour that plays well with chocolate. Or, use your favorite gluten free flour blend, although please note that the texture may not be the same.

A close up of seven gluten free chocolate cupcakes on a plate.

Storage Options

Make sure to bring the cupcakes to room temperature for at least 30 minutes before you serve them to help the cake and frosting relax and soften a bit, making for a better texture when you take a bite. Here’s how to store your gluten free chocolate cupcakes:

  • Fridge – To store, cover the cupcakes tightly with foil, or place them in an airtight container, and keep them in the fridge for up to 5 days.
  • Freezer – Freeze the cupcakes two ways: frosted cupcakes should be stored in an airtight freezer-safe container. Unfrosted cupcakes may be wrapped in a layer of plastic wrap and placed in a sealable freezer-safe bag. Store the cupcakes in the freezer for up to 3 months, and thaw them in the fridge before serving.

More Gluten Free Chocolate Cake Recipes

Gluten free chocolate cupcakes are arranged on a serving stand.

Gluten Free Chocolate Cupcakes

Nicole Spiridakis
Irresistible gluten free chocolate cupcakes are are unbelievably moist and tender. Top them with your favorite frosting for a handheld treat.
5 from 1 vote
Prep Time 10 minutes
Cook Time 45 minutes
Total Time 55 minutes
Course Dessert
Cuisine American
Servings 24 cupcakes
Calories 283 kcal


Chocolate Cupcakes

  • 2 ¼ cups gluten-free oat flour, 250 grams
  • 1 cup brown sugar
  • 1 cup sugar
  • ¾ cup unsweetened cocoa powder
  • 2 teaspoons baking soda
  • 1 teaspoon baking powder
  • 1 teaspoon fine sea salt
  • ½ cup coconut oil, melted
  • 2 eggs at room temperature
  • ½ cup Greek yogurt
  • ½ cup whole milk
  • 1 teaspoon pure vanilla extract
  • 1 cup fresh brewed hot coffee

Chocolate Frosting

  • ¾ cup unsalted butter, at soft room temperature
  • 4 ounces semisweet chocolate, melted
  • 2-3 cups powdered sugar, sifted
  • 1-2 tablespoons whole milk


  • Line two cupcake tins with liners and set aside.
  • In a medium bowl, whisk together the oat flour, sugars, cocoa powder, baking soda, baking powder, and salt.
  • In a large bowl, whisk together the coconut oil, eggs, yogurt, milk, and vanilla. Stir and whisk the dry ingredients into the wet ingredients and stir very well to combine. Stir in the coffee and stir until the batter is smooth and combined.
  • Divide the batter evenly between the cups and preheat the oven to 350°F. Let batter rest while the oven heats, about 15 minutes.
  • Place pans in the oven and bake for 30-35 minutes, checking at 30 minutes, until a toothpick in the center comes out clean and the sides are starting to pull away from the edges. Remove from oven and let cupcakes cool in the pans on a wire rack for 30 minutes, then turn out onto the rack to cool fully.
  • Frost cupcakes with chocolate buttercream.

Chocolate Buttercream

  • In a large bowl, cream the butter on medium speed. Add the powdered sugar, then the chocolate. Add milk 1 tablespoon at a time, keeping the mixer running, and beat until the frosting is smooth and fluffy.


Serving: 1cupcakeCalories: 283kcalCarbohydrates: 36gProtein: 5gFat: 15gSaturated Fat: 9gPolyunsaturated Fat: 1gMonounsaturated Fat: 3gTrans Fat: 0.2gCholesterol: 92mgSodium: 243mgPotassium: 144mgFiber: 2gSugar: 29gVitamin A: 298IUCalcium: 52mgIron: 1mg
Did you make this recipe?Let me know in the comments how it went!

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