The Best Sourdough Cupcakes Made With Fresh Milled Flour
These are truly the BEST sourdough Cupcakes! Whenever I bring them to a party or gathering, everyone asks how to make them. So, I mention they are made with sourdough, and all I get is shock and awe! The number one next comment is….”How did you get them so soft and moist? Everything sourdough I have ever had is so dense and chewy!” The next thing they are asking me is “Can you send me the recipe?” And, then that is followed up by, “Can I have some sourdough starter?” SO, as you can see, I had to post the recipe to share with the world!

The Best Sourdough Cupcakes Made With Fresh Milled Flour
The Best Sourdough Cupcakes ever! Every time we bring them to a gathering, everyone asks for the recipe! Although, these do take some time to make, it is mostly just resting time to allow the sourdough to ferment. You could make these all in the same day, mix them up, then bake if you are not looking for the dietary benefits of sourdough. So, either way, your guests will be impressed, and you will probably leave with an empty platter!
These cupcakes are so good! The deep chocolate flavor, with the cream cheese butter cream frosting is so good! This cupcake is so moist and delicious! We make them with fresh milled soft white wheat. So, we grind the flour fresh every time! You could make these with regular All-Purpose flour, but you may need to adjust the flour quantity slightly. Also, you can use your sourdough discard in any state, (fed or not.) That is another reason I LOVE this versatile recipe!
Why Do I Use Tea In This Recipe?
Well, there are a couple reason I use tea in this recipe. The first is because something with the tannins in the tea, just make this cupcake oh so decadent. Second, the black tea brings our the richness of the chocolate flavor. So, you may have heard this about coffee as well, but tea is a great alternative to this. I generally don’t have coffee in my house, because we are not really coffee drinkers. But, Tea is another story! We have tea up to my ears, because we drink it every single day, and in every single way!
Ingredients For The Best Sourdough Cupcakes Recipe:
Night Before (also pull out 1 cup of butter to soften)
- 2 cups Fresh Milled Flour (Mill 1&1/3 cups soft white wheat for this)
- 1/2 cup Olive Oil (You could use coconut oil too)
- 1/2 cup Sourdough Starter (at any stage)
- 1 cup Warm Black Tea (could use coffee or water)
Next Day
- 2 eggs
- 2 cups Sugar
- 1 tsp salt
- 2 tsp Vanilla (I love to make mine from scratch)
- 3/4 cup cocoa
- 1 cup whole milk
- 2 tsp baking soda This should be sprinkled in last
Frosting
- 1 cup softened butter (2 sticks)
- 8 oz softened cream cheese (I love to make mine from scratch)
- 2 tsp vanilla
- 1/4 tsp salt (if using unsalted butter)
- 4 cups Powdered sugar
Instructions For This Recipe:
THE NIGHT BEFORE
- Pull out 2 sticks of butter (1cup) to soften overnight
- Mix the flour, sourdough discard, olive oil, and tea in a bowl. Cover and allow to sit room temperature overnight up to 24 hours.
THE NEXT DAY
- Preheat your oven to 350F
- In a mixing bowl, mix together sugar, salt, vanilla, eggs, cocoa powder, and whole milk.
- Add your sourdough mixture into the sugar mixture. mix until incorporated.
- Sprinkle in the baking soda and mix in well
- Line your muffin tin, and add about 1/4 cup of batter to each one.
- Bake the cupcakes for 15-20 minutes, until a toothpick comes out without and batter pieces on it. Allow these to cool for 10 minutes, then remove from the pan to a cooling rack.
- Allow to cool completely before frosting them.
MAKE THE FROSTING
- In your mixer, add your softened butter, and begin to whisk.
- Then add the softened cream cheese until they are well combined.
- Now, add your vanilla and salt.
- Slowly whisk, and add in your powdered sugar 1 cup at a time.
- Once all the powdered sugar is incorporated, turn the speed up to medium. It should become nice and fluffy.
- Place in a piping(or ziplock) bag and pipe to your desire on your cupcakes.

Switching Your Sourdough Starter To Freshly Milled Flour
I have a post that I teach you how to switch your current sourdough starter over to fresh milled flour. Check it out HERE

Also, if you want to learn more about milling your own flour, I made a FRESH MILLED FLOUR 101 blog post course. It is FREE! So, I recommend starting there for your journey! Feel free to share this with anyone you know who wants to learn more, or is just getting started on the home ground flour journey!
WHAT DO I DO WITH THE EXTRA CUPCAKES?
If you are lucky enough to have extra cupcakes, they freeze so nicely. We just put the extra cupcakes frosted and all in the freezer on a sheet pan. Then, flash freeze them for 1 to 2 hours. Next, they can be stored in a freezer safe container or bag. So, when you want to eat them, just put however many you want on the counter to defrost. And, they defrost fairly quickly! Typically, It takes about 1 hour or less! I love to have extras, because whenever a craving hits, I have one available to me within arms reach! lol
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The Best Chocolate Sourdough Cupcakes Printable Recipe

The Best Chocolate Sourdough Cupcakes
Ingredients
Night Before (also pull out 1 cup of butter to soften)
- 2 cups Fresh Milled Flour (Mill 1&1/3 cups soft white wheat for this)
- 1/2 cup Olive Oil (You could use coconut oil too)
- 1/2 cup Sourdough Starter (at any stage)
- 1 cup Warm Black Tea (could use coffee or water)
Next Day
- 2 eggs
- 2 cups Sugar
- 1 tsp salt
- 2 tsps Vanilla (I love to make mine from scratch)
- 3/4 cup cocoa
- 1 cup whole milk
- 2 tsp baking soda This should be sprinkled in last
Frosting
- 1 cup softened butter (2 sticks)
- 8 oz softened cream cheese (I love to make mine from scratch)
- 2 tsp vanilla
- 1/4 tsp salt (if using unsalted butter)
- 4 cups Powdered sugar
Instructions
THE NIGHT BEFORE
- Pull out 2 sticks of butter (1cup) to soften overnight
- Mix the flour, sourdough discard, olive oil, and tea in a bowl. Cover and allow to sit room temperature overnight up to 24 hours.
THE NEXT DAY
- Preheat your oven to 350F
- In a mixing bowl, mix together sugar, salt, vanilla, eggs, cocoa powder, and whole milk.
- Add your sourdough mixture into the sugar mixture. mix until incorporated.
- Sprinkle in the baking soda and mix in well
- Line your muffin tin, and add about 1/4 cup of batter to each one.
- Bake the cupcakes for 15-20 minutes, until a toothpick comes out without and batter pieces on it. Allow these to cool for 10 minutes, then remove from the pan to a cooling rack.
- Allow to cool completely before frosting them.
MAKE THE FROSTING
- In your mixer, add your softened butter, and begin to whisk.
- Then add the softened cream cheese until they are well combined.
- Now, add your vanilla and salt.
- Slowly whisk, and add in your powdered sugar 1 cup at a time.
- Once all the powdered sugar is incorporated, turn the speed up to medium. It should become nice and fluffy.
- Place in a piping(or ziplock) bag and pipe to your desire on your cupcakes.
Video
Notes
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These cupcakes look amazing! They really make 36 full-size?
I have just put day 1 together.
Have you ever made it a a cake instead of cupcakes? I may get dating and do that tomorrow. Well let you know what happens. 😊
Yes, I typically get about 36 cupcakes, give or take a few. I make sure not to fill each one too full with batter, because they do rise quite a bit during baking. This would probably make a nice 9×13 sheet cake, or rounds. Just baking time will be longer. Let me know how it turns out. Thanks!
I can see how you would get 36 cupcakes! I put it in my largest Pyrex baking pan (when I looked for conversion, said 11×17, this is slightly smaller, ~10×15 inches, and worked well). Bake for 30 min, toothpick came out clean.
I used butter in place of oil.
For frosting, did 8 oz cream cheese, 1/4 c peanut butter, 1 tsp vanilla, 1/2 c Swerve, couple tablespoons cream. Doesn’t cover the cake as deeply as my family normally likes frosting, but got it to spread evenly anyway!
Next time I’m going to increase the amount of cocoa powder. I used the coffee.
Thank you so much! This was great fun. I took pictures but can’t figure out how to share with you.
That sounds amazing! Thank you for the update!