Chocolate Sourdough Cupcakes

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Simply decorated gluten-free chocolate sourdough cupcakes.

If you have a gluten-free sourdough starter, these Chocolate Sourdough Cupcakes will be a fun treat to bake! The decorating details will be up to you, but a dusting of organic powdered sugar with a drizzle of maple cream is simple to do and tasty without being too sweet!

With multiple food sensitivities and allergies, baking and eating cupcakes can be a rare occasion. I hope this recipe will inspire you to try something different! 

Consider baking half a dozen if you don’t need a full batch!

Inside of gluten-free chocolate cupcake.
A stack of gluten-free vegan chocolate cupcakes

Chocolate Sourdough Cupcakes

Developing this recipe was fun! It’s always a challenge to create a treat free of wheat/gluten, eggs, dairy, nuts, peanuts, legumes, corn, etc.

I kept the list of ingredients as simple as I could. The mixture includes gluten-free sourdough starter and good quality dark chocolate, organic raw cacao powder, coconut palm sugar, hemp milk, pure vanilla extract plus a few more.

If you enjoy all things sourdough, you should try baking these cupcakes!

Potato flakes used in gluten-free and vegan baking

Why Potato Flakes

One of the ingredients I fussed around with the most was the starchy component. I wanted to try something different so in went the potato flakes.

I did try baking a version with cooked mashed sweet potatoes but the potato flakes created a better texture. There’s absolutely nothing wrong with adding freshly mashed white or sweet potato but it does create a denser cupcake. If you were to try this option, I feel that half a cup of fresh mashed potatoes is enough.

Are there more substitutions for potato flakes? Great question! I did not try subbing potato starch or even potato flour in place of the flakes. If you were to try it I would definitely include less to start.

Keep in mind that this is a more expensive recipe to play around with. If you want to try various ingredients because of a potato allergy, consider baking half batches.

Homemade Hemp Milk

Fresh homemade hemp milk. It’s easy to make, it’s nutritious, and most people, even with a multitude of food sensitivities and food allergies can tolerate it.

To make 1 cup, it’s as simple as blending (in a high-speed blender) 1/3 cup of organic hemp seeds (hemp hearts) with 1-1/4 cups of water. You can squeeze the fresh milk through a nut mesh bag or a fine sieve to remove larger bits. It’s creamy, frothy and will keep in the fridge for a few days. 

If you love to learn by watching, I make fresh hemp milk at the beginning of this video.

Lightly decorated gluten-free vegan chocolate cupcakes.

Step-by-Step Video

The Process

The steps are simple but after you mix the GF sourdough starter with the flour and hemp milk you do need to rest/rise the mixture for at least a couple of hours.

Mixing GF sourdough starter with flour and hemp milk.

Once the first mixture is ready, you can combine the rest of the ingredients including the beautiful dark chocolate and raw cacao powder!

You can mix the chocolate mixture by hand or with a hand mixer. All the details are included in the instructions in the recipe card below.

Ingredients for GF chocolate cupcakes

You can gently fold in the starter mixture with the chocolate one or vice versa.

GF sourdough starter poured into chocolate cupcake mixture.

Grease each cupcake cavity with coconut oil and add a generous dusting of raw cacao powder. Doing so will make removing the bake cupcakes much easier. For this recipe, I preferred not using parchment paper cup liners.

Before and after pictures of gluten-free chocolate cupcakes in pan

Lastly, it’s always best to let cupcakes cool in the pan for 5 to 10 minutes. Then remove them from the pan and then finish cooling them on a rack before decorating them.

Decorate chocolate cupcakes with powdered sugar, maple cream or chocolate icing.

Decorating Ideas

I’ve been asking people on Instagram what they prefer, the cupcake part or the icing. Many like myself don’t enjoy frosting but some particularly love a deliciously sweet topping.

For this cupcake recipe, I favoured a super simple dusting of organic powdered sugar, but then I thought that it would be a fun idea to show you how to make a 1-ingredient maple cream icing.

A drizzle of homemade maple cream to decorate cupcakes.

Here are a few chocolate icing recipes from other bakers that are way better at creating tasty frosting recipes!

Cupcake decorated with maple cream and dark chocolate chips.
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Questions Before You Start?

The best way to ask your recipe questions is in the comments of this post (scroll to the bottom) or the Facebook group.

The group is a great place to ask allergen-friendly baking questions, get tips, inspiration and share recipes! Join our amazing and friendly Gluten-Free Vegan Baking by Fresh is Real Facebook Group

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Simply decorated gluten-free chocolate sourdough cupcakes.

Chocolate Sourdough Cupcakes

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 2 reviews
  • Author: Chantal | Fresh is Real
  • Prep Time: 20 minutes (2 hours rest time)
  • Cook Time: 22-25 minutes
  • Total Time: +/- 3 hours
  • Yield: 12 cupcakes 1x
  • Category: desserts
  • Method: Oven-Baked
  • Cuisine: Gluten-Free, Vegan, Plant-Based
  • Diet: Gluten Free


If you have a gluten-free sourdough starter, these Chocolate Sourdough Cupcakes will be a fun treat to bake! The decorating details will be up to you, but a dusting of organic powdered sugar with a drizzle of maple cream is simple to do and tasty without being too sweet!

With multiple food sensitivities and allergies, baking and eating cupcakes can be a rare occasion. I hope this recipe will inspire you to try something different! 

Consider baking half a dozen if you don’t need a full batch!


  • 1 cup freshly milled GF oat flour (100g)*
  • 1 cup sweet sorghum flour (100g)*
  • 1 cup homemade hemp milk (235g)** 
  • 3/4 cup GF brown rice sourdough starter, fed/active (215g)** 
  • 1 thin dark chocolate bar (80g)*** 
  • 1/2 cup boiling water
  • 1/2 cup potato flakes (25g)**** 
  • 1 cup coconut palm sugar (140g
  • 1/4 cup (4 tablespoons) coconut oil, soften/melted
  • 1/4 cup raw cacao powder (20g)
  • 2 tablespoons GF/CF/AF baking powder***** 
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon fine sea salt 
  • 2 teaspoons pure vanilla extract

Icing Ideas

1-Ingredient Maple Cream or a dusting of organic powdered sugar

Or here are some more options from other talented bakers:
chocolate glaze, chocolate ganache or chocolate vegan frosting


Step 1
To a large mixing bowl, sift the flour then add the GF starter and homemade hemp milk, mix well. Cover and let rest/rise for 2 hours.****** 

Step 2
After your mixture has rested for a couple of hours, proceed with preheating your oven to 350° F. Grease each cavity of your muffin pan with coconut oil and generously dust with cacao powder. You won’t need paper liners if you grease and dust your cavities. 

Step 3
In a separate large mixing bowl, add your dark chocolate (you can break it apart if it’s a thin bar), boiling water and mix until completely melted. Add the potato flakes to this mixture and continue mixing. Add remaining ingredients: coconut sugar, coconut oil, cacao powder, baking powder, baking soda, fine sea salt, and vanilla extract. Mix by hand (or a hand mixer) until everything is well combined. 

Step 4
Once your chocolate mixture is smooth, fold in the starter mixture from Step 1 and mix by hand until combined.

Step 5
Divide the batter between the 12 cupcake cavities. Bake 22-25 minutes until each top springs back when gently pressed. The tops might crack a little, but that’s ok. Wait 5-10 minutes, then remove each cupcake from the pan and finish cooling on a wire rack.

Step 6
You can dust the cupcakes with organic powdered sugar, spread with your favourite icing or make some yummy maple cream to drizzle over top! Enjoy! These cupcakes are best fresh!


This recipe creates enough batter for two 8-in round cakes. The baking time might need to be increased by 5 to 10 minutes. Remember to grease and line your baking pans with unbleached parchment paper. If you don’t have parchment paper, grease with coconut oil and add a generous dusting of cacao powder to prevent sticking. Cool your cakes in their pans for at least 20 minutes before flipping over onto a cooling rack to cool completely before icing.

*You can prepare freshly milled oat flour by blending/grinding gluten-free quick-cooking or large oats into a blender. I tested this cake with a brown rice starter. If you use a sorghum flour starter, you could consider swapping the sorghum flour in the cake ingredients for brown rice flour. 
**Homemade hemp milk: Blend (with blender) 1-1/4 cup water with 1/3 cup organic hemp hearts. Strain to remove larger bits. Plant milk subs: homemade oat, tiger nut or almond (if not allergic) milk could work well. Hemp milk is lighter than full fat coconut milk that can create a denser cupcake.
***I used one whole 6 x 3-in thin bar. I tried Blackout by alter eco. A deep 85% dark organic chocolate. Alternative: 1/2 cup (80g) of allergy-free dark chocolate chips.
****The potato flakes do create a lighter texture. A substitute would be 1/2 cup of cooked (boiled/steamed/roasted) and mashed white or sweet potatoes.
*****GF baking powder, also free of corn and aluminum. Ingredients: Baking soda, cream of tartar, tapioca flour. If your GF baking powder is different in ingredients and you’re not sure about the amount to use, try 1 tablespoon to start.
******You can let your batter rest/rise for longer than 2 hours (up to 5 hours) if you enjoy sourer tasting baked goods.


  1. Hi! In my country there´s no gluten free oats, do you think I can replace it with something else?

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    • Hi Sabina! Do you have almond meal/flour? It could work to keep the texture as light as possible. Please note that I did not try this alternative as of yet. The oat flour does help to bind the mixture. I wonder if you were to use almond meal/flour if you should also consider adding 1-2 tablespoons of flaxseed meal or ground flax seed to stick everything together.

      View Comment
  2. Thank you for the recipe and making each step clear. I made the cake version. I put crushed raspberries in the centre and iced the cake with a chocolate glaze. I cant have corn starch so I make my own baking powder from equal parts baking soda and cream of tartar

    Merci Chantal!

    View Comment
    • Kathy, thank you so much for trying this recipe and sharing your photos with me on Instagram! I really appreciate your feedback and rating! If anyone else tries to bake the cake version, Kathy did mention that she baked each layout for 35 minutes. If it’s ok Kathy, I would love to show your pictures in the GFV Baking by FiR Facebook group, your cake looked so good! You did a great job!

      View Comment
  3. Cindy McDermott

    I made these cupcakes and they are delicious! I followed the recipe as written except I used almond milk in place of hemp milk and I topped them with a simple ganache. I was so happy to find the AlterEco chocolate bar at my local Kroger too. They came out light and fluffy and the next day slightly dry but with heating for 15 seconds in the microwave made them just right. My husband loved these and I’ll definitely make then again!

    View Comment
    • Cindy! Thank you so much for sharing your feedback! I’m happy that you found the same dark chocolate! It’s great! It was my first time using it when creating this recipe! As for the dryness, I agree because there’s not much oil, no dairy, gluten or eggs a cupcake like this does dry much faster! I guess we’ll have to eat them faster 😉 I was debating whether or not to add more oil, but I find many prefer to avoid or reduce their oil consumption, so I left it as it was. Again, thank you for rating, commenting and sharing your pictures in the GFV Baking Facebook group—you’re awesome!

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  4. These look so tempting, I have never heard of sourdough cupcakes but yeah why not!
    Amaing pictures too!

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Make sure the ingredients you purchase are prepared in a facility free from the top allergens YOU AVOID. Gluten-free products should be certified GF and clearly labelled. Consult your medical professional with your dietary questions.

Even certified gluten-free ingredients such as GF oats, corn, seeds, etc., can create health problems for individuals following a GF diet. Always consult a medical professional if unsure about ingredients for your needs.