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Gluten-Free S’mores Cupcakes

These Gluten-Free S’mores Cupcakes are chocolate cupcakes baked in a buttery graham cracker crust. They’re filled with chocolate ganache and topped with a light and creamy homemade marshmallow frosting.

three s'mores cupcakes in a staggered line on the counter

Gluten-Free Chocolate Cupcakes with Marshmallow Frosting

Everyone loves a good s’more. Crunchy, buttery graham cracker, melty chocolate, gooey marshmallow…I mean, that flavor combination is incredible.

The only issue with traditional s’mores is that they’re messy so they’re not always super practical.

And that’s where these Gluten-Free S’more Cupcakes come in. These cupcakes are made using my gluten-free chocolate cupcakes base that’s baked in a graham cracker crust, filled with melty chocolate ganache, and topped with homemade marshmallow frosting.

They have all of the amazing flavors and textures we love about s’mores, but are neatly packaged in cupcake form!

Ingredients for S’mores Cupcakes

For the Crust

  • Graham Cracker Crumbs – you can make these by blending gluten-free graham crackers in your food processor. You could also use crushed Annie’s Gluten-Free Bunnies, gluten-free Oreos, or gluten-free chocolate chip cookies.
  • Melted Butter salted or unsalted

For the Cupcakes

  • Granulated Sugar
  • Vegetable Oil
  • Eggs
  • Vanilla Extract
  • Sour Cream – you could also use Greek yogurt or plain yogurt if preferred.
  • Gluten-Free Flour – I use Measure for Measure All-Purpose Gluten-Free Flour. Be sure you use that or something similar for the best results. Other gluten-free flours like almond flour or coconut flour will not work in this recipe.
  • Cocoa Powder
  • Baking Powder and Baking Soda
  • Salt
  • Brewed Coffee – hot brewed coffee adds moisture to the cupcakes and enhances the chocolate flavor. If you would prefer not to use coffee, feel free to swap it out for milk.

For the Ganache

  • Dark chocolate bar – use a bar of high-quality dark chocolate for the best flavor.
  • Heavy Whipping Cream

For the Frosting

  • Egg Whites – be sure you remove all of the yolk. The egg white is what creates that light meringue texture.
  • Granulated Sugar
  • Cream of Tartar – this is what helps stabilize the egg whites so the frosting can hold its structure.
  • Vanilla Extract

What Flour to Use for Gluten-Free Cupcakes

Use a measure for measure gluten-free flour that includes Xanthan gum. This means that 1 cup of all-purpose flour is replaced with 1 cup of gluten-free flour.

I like King Arthur Gluten-Free Flour, but Bob’s Red Mill is also a great option.

Can I Use All-Purpose Flour?

Yep! Since we’re using a measure for measure gluten-free flour, you can easily swap regular all-purpose flour in for gluten-free flour if that’s what you prefer.

side view of a s'mores cupcake topped with toasted marshmallow frosting

How to Make the Cupcakes

These gluten-free chocolate cupcakes look like a lot. But this recipe is actually pretty darn simple to throw together. And it’s definitely worth the time spent!

For the Crust

  1. Grind the crackers. Use a food processor and pulse the crackers until it resembles a fine crumb.
  2. Combine with Butter. Mix together the melted butter and crumbs until well coated.
  3. Fill the pan: Spoon 1 heaping tablespoon of the mixture into each section of a lined cupcake pan. Press the crust into the pan with a spoon, then set aside.

For the Cupcakes

  1. Combine the wet ingredients. In a large bowl, combine sugar, oil, eggs, and vanilla. Add in the sour cream and beat until fully combined.
  2. Add the dry ingredients and coffee. Pour in half of the dry ingredients and half of the coffee, mix until fully combined, then add in the rest of both.
  3. Portion the batter. Use a large cookie scoop to divide the batter into the cupcake pan with the crust. Fill each liner 2/3 full.
  4. Bake. Bake the cupcakes at 350ºF for 14-16 minutes or until a toothpick comes out clean. Remove from the oven and cool completely.

For the Ganache

  1. Melt the chocolate. Combine the chopped chocolate and heavy cream in a microwave-safe bowl. Microwave at 50% power for 60-90 seconds, stir until melted and smooth.
  2. Fill the cupcakes. Use a cupcake corer, melon baller, or knife to remove the centers of each cupcake. Fill each one with about 2 teaspoons of ganache, then set the cored piece of the cupcake back on top.

For the Frosting

  1. Separate the eggs. Separate the egg white from the yolks, making sure that no yolk is left in the whites or this can cause issues with the meringue.
  2. Combine the ingredients. In a clean stainless steel bowl, combine egg whites, sugar, and cream of tartar. Set the bowl over a pot with 1 1/4 cups water. Place over medium heat and whisk until the mixture reaches 140ºF and the sugar is dissolved.
  3. Beat the frosting. Immediately place the mixing bowl on your stand and beat on medium-high speed until stiff peaks form.
  4. Frost the cupcakes. Use a large open star tip or French tip to pipe the frosting onto the cooled and filled cupcakes. Optionally, toast the meringue with a handheld torch.

Tips, Tricks, and Recipe Notes

  • Spoon and level the flour. I always recommend using a kitchen scale to weigh the dry ingredients, but if it’s not available I recommend using the spoon and level method. Too much flour results in dry cupcakes.
  • Slowly melt the chocolate. When you’re melting the chocolate for the ganache, microwave it at 50% power. This helps prevent it from seizing up.
  • Frosting preparation: Before you make the frosting, clean the inside of the bowl with vinegar to remove any grease. Additionally, be sure that there is absolutely no yolk in your separated egg whites. This can cause the meringue not to set.
  • Swap the graham crackers. The gluten-free graham crackers are a classic s’mores ingredient, but you can totally use a different gluten-free cracker. Try Annie’s GF Bunnies, gluten-free Oreos, or gluten-free chocolate chip cookies instead.
gluten-free s'mores cupcake with a bite taken out

How Far in Advance Can I Make These?

If you want to get ahead with this recipe, you can prep the cupcakes ahead of time and add the ganache and frosting later on. Simply prep and bake as directed, cool completely and store in an air-tight container at room temperature for 2 days or in the freezer for up to 1 month.

When you’re ready to serve them, thaw in the fridge, then add the ganache and topping.

How to Store Finished Cupcakes

Frosted s’mores cupcakes will last in an airtight container on the counter for 2 days.

overhead shot of two halves of a s'mores cupcake laying on the counter side by side
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closeup of a frosted s'mores cupcake

Gluten-Free S’mores Cupcakes

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
  • Author: Julianne Dell
  • Prep Time: 30 minutes
  • Cook Time: 14 minutes
  • Total Time: 44 minutes
  • Yield: 12 cupcakes
  • Category: Desserts
  • Method: Baked


These Gluten-Free S’mores Cupcakes are chocolate cupcakes baked in a buttery graham cracker crust. They’re filled with chocolate ganache and topped with a light and creamy homemade marshmallow frosting.


For the Crust

  • 1 ¼ cups (150g) gluten-free graham cracker crumbs 
  • 3 tablespoons (42g) unsalted butter, melted

For the Cupcakes

  • ¾ cups (143g) granulated sugar
  • ¼ cup (59ml) vegetable oil
  • 2 large eggs
  • 2 teaspoons (10ml) pure vanilla extract
  • ¼ cup (59ml) sour cream
  • 1 cup (164g) measure for measure all-purpose gluten-free flour sifted
  • ¼ cup (28g) natural cocoa powder
  • 1 ¼ teaspoons (5.6g) baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon salt
  • ⅔ cup (157ml) hot brewed coffee

Ganache Filling

  • 3 ounces dark chocolate, chopped
  • 6 tablespoons (90ml) heavy whipping cream

For the Frosting

  • 4 large egg whites
  • 1 cup (190g) granulated sugar
  • ½ teaspoon cream of tartar
  • 1 teaspoon (5ml) pure vanilla extract


For the Crust

  1. Preheat the oven to 350°F. Line a cupcake pan with cupcake liners.
  2. Prepare the crust. Grind the gluten-free crackers into a fine crumb using a food processor. Combine with melted butter and stir until well combined. 
  3. Spoon 1 heaping tablespoon of the graham cracker mixture into each cupcake liner, and press into the pan with a spoon. Set aside. 

For the Cupcakes

  1. In a large mixing bowl, combine the sugar, vegetable oil, eggs and vanilla extract. Beat on medium speed until the eggs and oil are well incorporated and the batter is lighter in color. Next mix in the sour cream and beat until well combined.
  2. In a separate bowl, sift together the dry ingredients. Alternating adding half the dry ingredients with half the coffee, mixing until combined. Repeat until all ingredients are added. Use a spatula to scrape down the sides of the bowl and stir the batter from the bottom to the top to ensure it’s well mixed.
  3. Using a large cookie scoop, divide the batter evenly, filling each liner 2/3 full. Bake at 350°F for 14-16 minutes. Test the cupcakes for doneness by inserting a toothpick into the center of the cupcake. If the toothpick comes out clean, the cupcakes are done. Cool Completely.

For the filling

  1. Combine the chocolate and heavy cream in a microwave-safe bowl. Microwave at 50% power for 60-90 seconds. Allow it to sit for about 1 minute before stirring and then stir until it’s completely smooth.
  2. To fill the cupcakes with the ganache, remove the centers using a cupcake corer, a melon baller or a knife. Fill each one with about 2 teaspoons of ganache. Place a piece of the cupcake you removed back on top of the ganache.

For the frosting

  1. Separate the egg white from the yolks, and ensure no yolks are mixed in with the whites. Wipe down the inside of your stainless-steel bowl with vinegar to remove any grease. 
  2. Combine egg whites with sugar and cream of tartar in the bowl with a candy thermometer attached. Set the bowl over the top of a pot with 1 ¼ cups water covering the bottom. Place over medium heat.
  3. Stir constantly with a whisk until the mixture reaches 140°. The sugar should be dissolved in the egg whites. 
  4. Immediately place the mixing bowl on your stand. Using the wire whisk attachment, beat the mixture on medium-high speed until it reaches stiff and glossy peaks. The bowl should be cool to the touch.
  5. Pipe the cupcakes with a large open star tip or french tip. Toast the meringue with a handheld torch.


  • Serving Size: 1 cupcake
  • Calories: 358
  • Sugar: 35 g
  • Sodium: 261.7 mg
  • Fat: 13.9 g
  • Carbohydrates: 55 g
  • Fiber: 2.2 g
  • Protein: 4.9 g
  • Cholesterol: 45 mg

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13 thoughts on “Gluten-Free S’mores Cupcakes”

  1. Absolutely amazing recipe! I changed it a bit therefore not gluten free. Added speculoos cookies to the graham cracker base and only had AP flour. I didn’t use the microwave – did 3oz of whipping cream warmed in the stove and then poured over 3oz of chopped chocolate – let it stand for 2 mins and then stirred to combine. I don’t trust my microwave. Everything else was the same. Super flavorful. The frosting is to die for!

  2. Avatar photo
    healthy chocolate

    Hi would you mind stating which blog platform you’re using?
    I’m planning to start my own blog in the near future but I’m
    having a tough time deciding between BlogEngine/Wordpress/B2evolution and Drupal.

    The reason I ask is because your design seems different then most blogs and I’m looking for something unique.
    P.S Sorry for getting off-topic but I had to ask!

  3. Avatar photo
    Lauren @ Climbing Grier Mountain

    Yay!!! So glad you liked the frosting! I was a doubter too about the whole microwave thing, but it really works! I can’t wait to make these guys!

    1. Avatar photo

      Thanks for the awesome recipe Lauren! Now I am counting the various recipes I want to try with it!

  4. I love whisk shots too!! And yours is gorgeous. And these cupcakes? Even more beautiful! I love s’mores. That frosting is a must try.

    1. Avatar photo

      Hi Sally, thank you! Yes, these are cupcakes, I baked them in a special liner to create the shape.

  5. I’m gonna try these on my gluten AND non-gluten friends. Nicely presented! I was so jealous of the person who took the bite of that cupcake in photo numero 4.