These vegan and Gluten Free Chocolate Cupcakes are super moist, fluffy, and extra decadent! They’re rich in chocolate flavor with vegan chocolate chips studded throughout and are topped with a luscious vegan chocolate buttercream frosting.

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Gluten Free Chocolate Cupcakes Recipe
These may just be the BEST chocolate cupcakes you’ve ever had! Soft, light, sweet, and incredibly rich and chocolatey — you’ll forget they’re refined sugar-free, gluten-free, and vegan!
The combination of the gluten-free oat flour and the liquid ingredients creates the perfect amount of moisture while keeping the cupcakes fluffy and tender. Cacao powder creates a deep chocolate flavor, with dairy-free chocolate chips adding melty chocolate goodness in every bite.
Did I mention they’re super indulgent? I made them double chocolate cupcakes and frosted them with a chocolate version of my vegan vanilla buttercream icing. Perfect for chocolate lovers, these cupcakes are an irresistible treat you won’t be able to get enough of!
Looking for more gluten-free dairy-free chocolate treats? Try my Gluten Free Chocolate Cake, Ice Cream Sandwiches, Gluten Free Yule Log or these Fudgy Gluten Free Vegan Brownies.

Ingredients
See the recipe card below for ingredient quantities.
Chocolate Cupcakes
- flaxseed meal – also called ground flaxseed.
- gluten free oat flour – if making your oat flour from scratch, ensure it’s finely ground.
- raw cacao powder
- coconut sugar
- baking soda
- sea salt
- non-dairy milk – use any kind of dairy-free milk, ensuring it’s at room temperature.
- avocado oil
- maple syrup
- vanilla extract
- hot coffee – amplifies the chocolate flavor without leaving a noticeable coffee flavor. You can use any coffee you’d like, including brewed, instant, or even decaf!
- vegan chocolate chips – I love the Pascha brand. Most dairy-free chocolate chips I’ve seen available are vegan, but you should check the ingredients to be sure.
Vegan Chocolate Buttercream Frosting
- palm shortening
- tapioca starch
- cacao powder
- maple syrup
- vanilla extract
- pinch of sea salt

Ingredient Substitutions
- You can substitute avocado oil with olive oil or another neutral-flavored oil.
- If you’d like, use maple sugar instead of coconut sugar, or a granulated sugar if you don’t need this to be refined sugar free.
- You can use just boiled water instead of the coffee.
- I don’t recommend any other substitutions.
How to Make Gluten Free Chocolate Cupcakes
Step 1. Make Flax Egg
In a small cup or bowl, whisk together the flaxseed meal and water. Set aside to thicken.
Step 2. Make the Cupcake Batter
Combine the dry ingredients.


Next, combine wet ingredients except the coffee.

Combine dry and wet ingredients. Then stir in coffee until just combined.


Fold in chocolate chips.

Step 3. Transfer Batter
Fill lined muffin tin 3/4 way full.


Step 4. Bake
Bake in middle rack of oven preheated to 350F for 18 minutes.


Step 5. Cool
Allow cupcakes to cool completely.
Step 6. Frost the Cupcakes
Make the vegan chocolate buttercream frosting in a stand mixer, food processor, or in a bowl with a handheld mixer or whisk.
Frost the cupcakes as desired.

Tips & Tricks
Use Room Temperature Ingredients
Use room temperature wet ingredients for both the batter and frosting to ensure smooth and even mixing and to prevent curdling. Allow any refrigerated ingredients such as the dairy-free milk and maple syrup to come to room temperature, or gently warm cold liquids in the microwave before cooling to room temp. However, note the coffee should be hot!
Filling the Liners
Only fill the liners up to 3/4 way full so that the cupcakes rise just above the top of the liner. Use a large cookie or ice cream scoop or spoon to evenly divide the batter.
Avoid Over-mixing
Don’t over-mix the batter to maintain the cupcakes’ light and fluffy texture. Mix the wet and dry ingredients together until just combined and gently fold in the flax egg and chocolate chips to avoid overworking the batter, which can result in tough, dense, or rubbery cupcakes.
Avoid Over-baking
Don’t dry out the cupcakes by over-baking them. Check for doneness by sticking a toothpick into the center of a cupcake. It’s ready when the toothpick comes out clean or with a few moist crumbs.
Allow Cupcakes to Fully Cool
As with all gluten-free baked goods, allow the cupcakes to cool completely before frosting so they set fully and don’t crumble, and so they don’t melt the icing. However, reheating them slightly before serving enhances the texture and brings out the flavor, especially after storing in the fridge.
Decorating the Cupcakes
Feel free to frost the cupcakes with tall swirls, a rose pattern, any design you like! Add some dairy-free chocolate sprinkles or chocolate shavings for even more chocolatey goodness.
You can decorate them for special occasions and holidays, like these Halloween Ghost Cupcakes!
Omit the cacao powder to make my original Vegan Buttercream Frosting, being sure to add lots of tapioca starch until stiff peaks form. Pipe three circles on the cupcakes to make the ghost’s body and use two chocolate chips for the eyes.


Frequently Asked Questions
I don’t recommend preparing the cupcake batter in advance and refrigerating or freezing to bake later. It should be made just before baking to ensure optimal rise and texture.
Unfortunately, no. This cupcake recipe uses gluten-free oat flour, a grain eliminated in both Modified and Core AIP. For AIP-compliant cupcakes, try my Spiced Apple Cupcakes or these Lemon Olive Oil Cupcakes.
For AIP chocolate desserts, try these Baked Chocolate Donuts, Chocolate Peppermint Cookies, Crinkle Cookies or my Fudgy Gluten Free Vegan Brownies and Gluten Free Yule Log for Modified AIP.

Storage Instructions
- Room Temperature: If unfrosted, you can store these gluten-free cupcakes in an airtight container for 1-2 days.
- Fridge: Especially once frosted, I recommend storing these cupcakes in a large, airtight container in the fridge for up to 5 days.
- Freezer: Store unfrosted cupcakes in the freezer for 2-3 months. Thaw in the fridge overnight and allow to come to room temperature before frosting.

As the creator of an online dairy-free and gluten-free baking school, I understand how challenging it is to find dairy and gluten-free desserts that taste as delicious as their conventional counterparts. That’s why you’ll love my Vegan Gluten-Free Chocolate Cupcakes with their rich chocolate flavor and moist, soft texture, made completely without gluten, dairy, or eggs! If you do, I would appreciate it if you would give the recipe a rating and review. Be sure to snap a picture of the finished product and share it with me on Instagram by tagging @healmedelicious and using the hashtag #healmedelicious.
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Gluten Free Chocolate Cupcakes Recipe (Vegan)
- Total Time: 33 minutes
- Yield: 12 cupcakes 1x
- Diet: Gluten Free
Description
These Vegan and Gluten-Free Chocolate Cupcakes are moist, fluffy, and super rich! With chocolate chips in every bite and a luscious vegan chocolate buttercream frosting, they’re the ultimate treat, perfect for any chocolate lover!
Ingredients
Chocolate Cupcakes
- 1 TBSP flaxseed meal
- 3 TBSP water
- 1.5 cups gluten free oat flour, finely ground
- 2/3 cup raw cacao powder
- 1/4 cup coconut sugar
- 1 tsp baking soda
- 1/4 tsp sea salt
- 1/2 cup dairy free milk, room temperature
- 3 TBSP avocado oil
- 1/4 cup + 1 tbsp maple syrup
- 2 tsp vanilla extract
- 1/2 cup hot coffee
- 1/3 cup vegan chocolate chips
Chocolate Buttercream Frosting
- 2 cups palm shortening
- 1/2 cup tapioca starch
- 6 TBSP cacao powder
- 1/2 cup maple syrup
- 2 tsp vanilla extract
- pinch of sea salt
Instructions
- Preheat the oven to 350F and line a cupcake pan or muffin tin with 12 non-stick liners.
- In a small bowl or cup, use a fork to whisk together flaxseed meal and water. Set aside to congeal into a gel-like consistency, at least 5 minutes.
- In a large bowl, combine oat flour, cacao powder, coconut sugar, baking soda, and sea salt. Then make a well in the center of the dry ingredients.
- In a separate bowl, combine dairy-free milk, avocado oil, maple syrup, and vanilla extract. Then, fold in the flax egg.
- Pour the wet ingredient mixture into the center of the dry ingredient mixture, and stir until just combined.
- Pour in the hot coffee and stir until just combined.
- Gently fold in the vegan chocolate chips.
- Using a large scoop or spoon, evenly distribute the cupcake batter into the liners, filling each liner until 3/4 full.
- Bake in the middle rack of the preheated oven for 18 minutes.
- Remove from oven and place cupcake pan on a wire cooling rack. Allow cupcakes to cool completely before frosting.
Vegan Chocolate Buttercream Frosting
- In a stand mixer, food processor, or in a deep bowl with a handheld mixer, wire whisk, or spatula, combine palm shortening, tapioca starch, cacao powder, maple syrup, vanilla extract, and pinch of sea salt. Whisk or pulse until combined.*
Decorate the Cupcakes
- Transfer the chocolate frosting to a piping bag or a plastic food storage bag with one corner cut off.
- Pipe the frosting in whatever style or pattern you like.
Notes
*If making the frosting in advance, store in the fridge. Allow to come to room temperature and whisk once more before icing the cupcakes.
- Prep Time: 15 minutes
- Cook Time: 18 minutes
- Category: Desserts
- Method: Baked
- Cuisine: American
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