Prepare yourself for the absolute best gluten free chocolate cupcakes! They're moist and soft with the most delicious and easy chocolate cream cheese frosting. With bold chocolate flavor and the perfect cupcake texture, nobody will ever guess they're gluten free!
There is no better way to celebrate something big or small than with a batch of cupcakes! They're cake's cutter little sis and so versatile. These delicious cupcakes have both a deep chocolate cake base and a creamy chocolate cream cheese frosting on top any chocolate lover can't pass up.
If you're looking for a cupcakes that don't have gluten or dairy, check out my gluten free and dairy free chocolate cupcake recipe that is adapted from my gluten free chocolate cake recipe which uses a combination of almond flour and tapioca flour.
Ingredients and Substitutions
For the gluten-free cupcakes
- Eggs - Large eggs at room temperature are needed to help the cupcakes rise in the oven.
- Granulated sugar - Adds sweetness to the cupcakes.
- Brown sugar - You can also use coconut sugar. Both will add a deep caramel flavor to the chocolate.
- Coconut oil - Any lightly flavored oil like vegetable oil will work in this recipe or melted butter. Make sure it's melted but has cooled down for a few minutes before adding it to the mixing bowl.
- Milk - Any type of milk will work in this recipe. I used almond milk.
- Apple cider vinegar - A non-traditional ingredient in cupcakes but necessary in a lot of gluten free baking recipes. The acidity will help to activate the baking powder and soda so the cupcakes rise well in the oven. You won't taste it in the cupcakes, I promise! If you use buttermilk as your milk, you don't need to add apple cider vinegar.
- Gluten free 1:1 flour - I like King Arthur or Bob's Red Mill gluten-free flour blend.
For the frosting
- Cream cheese - Make sure it's soft and at room temperature. Block cream cheese works best, not the spreadable kind in the tub.
- Butter - Set this out for at least 30 minutes to soften the butter.
- Powdered sugar - Sift your powdered sugar for extra silky smooth perfect texture.
- Cocoa powder - Provides some chocolate flavor to the frosting.
How to Make Gluten free Chocolate Cupcakes
You will need an electric mixer or stand mixer and a large mixing bowl as well as a cupcake pan. If you have a piping bag with a tip, great! If not, you can also just use a knife to spread the frosting on top.
Step 1 : Mix the wet ingredients and sugar. This includes everything except the milk which comes later. In a large bowl add the eggs, white sugar, brown sugar, coconut oil, and vanilla extract. Mix well with a mixer or stiff whisk until the sugar is well incorporated.
Step 2 : Add the milk and apple cider vinegar. Pour in the milk and apple cider vinegar and continue to mix well to incorporate.
Step 3 : Add the dry ingredients. Sprinkle in the gluten free flour, cocoa powder, baking powder, and baking soda. Gently fold the flours into the cupcake batter with a rubber spatula until no flour clumps remain.
Step 4 : Bake! Use a cookie scoop to scoop the cupcake batter into a cupcake tin with cupcake liners. Fill each cupcake liner up about ¾ of the way full. Because theses are gluten free cupcakes, they won't rise like traditional cupcakes so we can fill the liners up more than we normally would.
Bake the pan in the oven until the cupcakes have risen and have a nice dome on top. Insert a toothpick into the center of one to make sure it comes out clean. If the toothpick still has some cupcake batter on it, the pan needs a little more time in the oven.
Once the cupcakes are done, let them cool for a few minutes in the pan and then transfer them to a wire rack to cool completely. This will prevent the muffin bottoms from getting wet and soggy.
Step 5 : Prepare the frosting. In a medium bowl beat the butter and cream cheese well until light and creamy. This can take about 5 - 7 minutes. Slowly add the powdered sugar in ½ cup increments. Once half of the powdered sugar is mixed in, add the cocoa powder and vanilla and 1 tablespoon of milk. Continue to add the rest of the powdered sugar in ½ cup increments until you reach the desired consistency.
Step 6 : Assemble the cupcakes. Once the cupcakes have cooled completely, fill a pastry bag fitted with a tip with the chocolate frosting. You can also use a butter knife to spread the frosting on top of the cupcakes if you don't have a piping bag.
Start in the middle of the cupcake and pipe a big swirl on top of the cupcake. Top with shaved chocolate or sprinkles if desired and enjoy!
How to Store
After the cupcakes are all frosted, store the cupcakes in an airtight container in the fridge where they will keep for up to 4 days. Store them in the fridge so the cream cheese frosting doesn't get too soft and runny.
You can also prepare the cupcakes beforehand and frost them at a later date. Store the unfrosted cupcakes in an airtight container in the fridge and then make the frosting when you're ready!
- Don't over mix the batter. Even though this is gluten free cupcake batter, you can still over do it on the mixing which can lead to stiff, not-so-moist, cupcakes. Fold the batter until the flour is just incorporated.
- Fill the cupcake liners ¾ of the way full for best results. This may be a little more than you would with traditional cupcakes.
- Make sure your oven is calibrated correctly at 350 F. I say this mainly because I discovered (while testing this recipe!) that my oven was running too hot. I would set it to 350 F but it was actually more like 370 F! This gave me perfectly domed cupcakes but the middle was too raw since it didn't have enough time to cook through. At 350 F the cupcakes will rise just right and the middle will bake through properly.
- Sift the powdered sugar and cocoa powder for the frosting if you want a silky smooth chocolate frosting on top of each cupcake!
Frequently Asked Questions
Yes, simply swap the gluten free 1:1 flour with all purpose flour and follow the directions as written.
Store the cupcakes in an airtight container in the fridge. This will keep the cupcakes moist and flavorful. Let them thaw for a few minutes at room temperature when ready to enjoy.
Without icing, these cupcakes can sit out at room temperature for about 5 days before they start to dry out. If you add frosting on top though, you will want to keep them in the fridge so the icing doesn't get too soft. They will be fine at room temperature for 2 - 3 hours.
Check out these recipes for more chocolate treats
PS : If you make this recipe, be sure to leave a star review and comment below! Also be sure to follow along with me on Instagram and Pinterest to stay up to date on all tasty recipes here at The Fit Peach!
The Best Gluten free Chocolate Cupcakes
For the cupcakes
- 2 eggs
- ⅔ cup sugar
- ⅓ cup brown sugar - or coconut sugar
- ⅓ cup coconut oil - melted, or other neutral oil
- 1 teaspoon vanilla extract
- ⅔ cup milk - any type of milk will work
- 1 tablespoon apple cider vinegar
- 1 cup gluten free 1:1 flour
- ½ cup cocoa powder
- 1 teaspoon baking powder
- ¼ teaspoon baking soda
For the frosting
- 8 oz cream cheese - softened at room temperature
- ½ cup butter - softened
- 3 - 4 cups powdered sugar - sifted
- ⅓ cup cocoa powder
- 1 teaspoon vanilla extract
- 1 - 2 tablespoon milk - any type of milk will work
- Shaved chocolate - to garnich, optional
- Preheat oven to 350 F. In a large bowl add the eggs, sugar, brown sugar, melted coconut oil, and vanilla extract. Mix well with an electric mixer, stand mixer, or stiff whisk until the sugar is dissolved.
- Pour in the milk and apple cider vinegar and mix well to distribute into the batter.
- Add the gluten free flour, cocoa powder, baking powder, and baking soda to the bowl and gently fold into the batter with a rubber spatula until the flour is just incorporated. Be careful not to over mix!
- Place cupcake liners in a cupcake tin. Use a cookie scoop or spoon to fill the liners up about ¾ of the way full. Tap the cupcake pan on the counter a few times to release any air bubbles. Bake in the oven for 15 - 17 minutes until the cupcakes are perfectly domed on top and you can insert a toothpick into the center of a cupcake and it comes out clean.
- Let the cupcakes cool slightly in the pan before transferring them to a cooling rack to cool completely. This will prevent wet and soggy cupcakes.
- Once the cupcakes have cooled down, prepare the icing by creaming the cream cheese and butter together in a mixing bowl with a mixer. Do this for at least 5 minutes until the cream cheese and butter are creamy and no clumps of cream cheese are left.
- Add the powdered sugar to the bowl in ½ cup increments and continue mixing. Once half of the powdered sugar has been added, add the cocoa powder, vanilla extract, and 1 tablespoon of milk. Continue to mix and add the remaining powdered sugar in ½ cup increments until you reach your desired consistency.
- Fill a piping bag fitted with a tip with the frosting. Start in the middle of each cupcake and pipe a large swirl on top of each cupcake. Top with shaved chocolate if desired and enjoy!