Double Chocolate Sourdough Muffins with Einkorn Flour
Nothing beats a morning with fresh homemade muffins. Costco muffins ain’t got nothing on these double chocolate Sourdough muffins made with einkorn. Not only are they mouth wateringly wonderful, they’re full of nutrition and protein to energize your day!

Double chocolate einkorn muffins with sourdough are moist, chocolatey and filled with the best rich taste! If you are on the hunt for a double chocolate muffin recipe, then you’ve come to the right place! These are perfect to mix up to have on hand for the week and work well for a quick grab for breakfast, a yummy healthy snack or even for a little something sweet in the evenings.
These can be made ahead of time and packaged or froze in individual baggies for lunches or a quick grab and go snack needed anytime!
Special Ingredients for Double Chocolate Muffins
This recipe for double chocolate sourdough muffins with Einkorn flour, uses two special ingredients that we will look at more specifically: Einkorn flour and Sourdough starter.
Each of them offer both added nutritional benefits and amazing distinct flavor. Together, these complement each other well and make a delicious, rich and moist chocolate muffin.
These double chocolate muffins are a healthy option since they use maple syrup as one of the sweeteners. For the other sweetener you can use your preference whether you want conventional brown sugar or a replacement of choice.

Sourdough Starter Benefits
If you have sourdough starter needing to be used up, this is the perfect recipe to make! You can use active (fed) starter or sourdough discard. Either will work fine in this recipe! You can use any starter you have on hand – no specific flour type is needed for this recipe. If it is fed with white flour that is fine! It doesn’t need to be specific Einkorn fed sourdough starter.
Adding sourdough starter to your Einkorn cookies offers several nutritional benefits plus it gives a wonderful familiar ‘tang’ to the baked good.
Sourdough is the process of fermentation by the natural use of lactic bacteria acid which is the natural yeasts in the environment around us.
Sourdough supports gut health and digestibly by the process of breaking down the complex carbohydrates and proteins, and increasing the prebiotics which make it easier for our bodies to digest. It also feeds healthy bacteria to the gut, which in turn supports so many other aspects of our health!
Whole Wheat Einkorn Benefits
Einkorn is a true form of wheat that has not been genetically altered and it also carries much more nutrition and protein than modern day wheat. It is the world’s very first wheat. You can see the nutritional information HERE and it’s anti-inflammatory aspects HERE. The downside is that einkorn tends to be a much more dense grain (due to all that good nutrition), making it harder to work with.
The gluten structure has also changed. If you’re sensitive to or know someone sensitive to gluten, you’ll know that modern day’s wheat gluten can cause stomach ailments, especially if not used fresh ground. Einkorn wheat, on the other hand, has a much weaker gluten structure. It won’t stretch and rise as much as other flours, but your stomach will thank you!
HERE are several essential tips for baking with this ancient grain.
Are Fresh ground Einkorn and Whole Wheat Einkorn the same?
The short answer is, no they are not the same! Grinding your grain to use fresh is becoming a more common and heard of routine that’s being incorporated into home baking.
To receive the full nutritional benefits of whole wheat and ancient grains, you MUST mill the actual grain and use the flour fresh!
Think of fresh ground flour as being “complete” and “alive”, and store bought flour that comes ground as “dead-flour”. When the grain is ground fresh, you are getting vital nutrients, vitamins and minerals that are sorely depleted in store-bought flour.
We’ve found huge benefits for our immune and gut health while consistently incorporating fresh ground goodies made with the original wheat einkorn.
Here, you can check out all you need to know about Einkorn and its health benefits.
Maple Syrup Benefits
Maple is one of the best combinations with chocolate and suites this recipe perfectly. It doesn’t take over the chocolate flavor but helps develop the deep richness of it.

Where to Buy Einkorn Flour
Einkorn can be on the pricey side and increasingly more difficult to source. It is not often found in your typical grocery store, and if it is, then you have to deal with higher costs.
I like to buy in bulk – it not only is more cost effective but that way I have more readily on hand and am less likely to run out.
Store your bulk Einkorn grain in plastic buckets with lids. Keep a smaller amount handy by your milling area in your kitchen and refill your canister as needed!
Here’s My Favorite Places to Get Einkorn Berries and Flour.
Tip: Keep multiple sources in mind for purchasing your Einkorn. This not only helps with comparing prices (it can vary) but also if it’s not available from one source, then you have a back up option and can try the next place.
Did you know that most of the time, the whole wheat berries (grain kernels) are actually cheaper than purchasing the ground flour? Investing in a Mockmill 100 would be such a great idea if you are wanting to benefit and give your family the additional and full healthy benefits of the grain.
Recipe for Double Chocolate Sourdough Einkorn Muffins
This recipe offers measurements both in cups and ml or grams. Read the ingredient listing carefully so you don’t confuse the ml or gram amounts.
Mix Wet Ingredients
1/3 Cup or 2 oz melted coconut oil or oil of choice
1/2 Cup or 120 ml milk
1/2 Cup or about 140 ml Sourdough Starter
1/2 Cup or 80 g brown, maple or coconut sugar
1/2 Cup or 118 ml Maple Syrup
4 large eggs
1/3 Cup or 30 g Cocoa Powder
Add in Dry Ingredients
2 1/4 Cups or 270 g Whole Wheat Einkorn Flour ( I use Freshly Ground)
1 teaspoon or 6 g Sea Salt
2 teaspoons or 8 g Baking Powder
1/2 teaspoon or 4 g Baking Soda
3/4 Cup or 140 g Chocolate Chips
Rest Batter
With this recipe, you have the option to allow the batter to rest and long ferment overnight in the fridge, or to bake them right away.
Allowing the batter to rest will give you the real benefits of the sourdough starter (more than just baking right away and getting the sourdough taste).
Having the batter refrigerated and fermenting until ready to use, also is a great option for having a fresh muffin for breakfast without having to bake on top of everything else there is to do in the morning rush!
Bake the Muffins
In a stand mixer with the beater attachment combine oil, sourdough starter, maple syrup and brown sugar. Beat on medium speed for one minute.
Add in milk, eggs and cocoa powder. Beat on high for 2 more minutes until creamy and frothy.
Add in dry ingredients starting with the Einkorn flour. Mix on low until ingredients gently come together. Do not over mix.


Remove bowl from the mixer. Using a spatula, fold in chocolate chips reserving a handful to sprinkle on muffin tops.
Cover and allow batter to sit in the refrigerator for a few hours to overnight. Alternatively, you can bake immediately.
To prepare for baking, heat oven to 450 degrees Fahrenheit.
Generously grease muffin tin or insert muffin cup liners. Fill muffin cups with batter, then sprinkle on reserved chocolate chips over the tops. Gently press the chocolate chips into batter to hold in place and prevent burning.
Bake for 18-22 minutes. Let cool for a couple minutes before transferring to a cooling rack. Enjoy!
Einkorn Flour Double Chocolate Sourdough Muffins
A rich and filling muffins full of nutritious einkorn and risen with sourdough starter.
Ingredients
- Wet Ingredients
- 1/3 Cup or 2 oz melted coconut oil or oil of choice
- 1/2 Cup or 120 ml milk
- 1/2 Cup or about 140 ml Sourdough Starter
- 1/2 Cup or 80 g brown, maple or coconut sugar
- 1/2 Cup or 118 ml Maple Syrup
- 4 large eggs
- 1/3 Cup or 30 g Cocoa Powder
- Dry Ingredients
- 2 1/4 Cups or 270 g Whole Wheat Einkorn Flour ( I use Freshly Ground)
- 1 teaspoon or 6 g Sea Salt
- 2 teaspoons or 8 g Baking Powder
- 1/2 teaspoon or 4 g Baking Soda
- 3/4 Cup or 140 g Chocolate Chips
- oil for greasing muffin tin or muffin cup liners
Instructions
- In a stand mixer with the beater attachment combine oil, sourdough starter, maple sugar and brown sugar. Beat on medium speed for one minute. Add in milk, eggs and cocoa powder. Beat on high for 2 more minutes until creamy and frothy.
- Add in dry ingredients starting with einkorn flour. Mix on low until ingredients gently come together. Do not over mix.
- Remove bowl from Mixer. Using a spatula, fold in chocolate chips reserving a handful to sprinkle on muffin tops. Cover and allow batter to sit in refrigerator for a few hours to overnight. Alternatively, you can bake immediately.
- To prepare for baking, heat oven to 450 degrees Fahrenheit. Generously grease muffin tin or insert muffin cup liners. Fill muffin cups with batter, then sprinkle on reserved chocolate chips over the tops. Gently press the chocolate chips into batter to hold in place and prevent burning. Bake for 18-22 minutes. Let cool for a couple minutes before transferring to a cooling rack. Enjoy!
Notes
- You can bake these muffins immediately or, for better rise, allow to sit several hours to overnight.
- Feel free to exchange a non dairy milk or oil to make these dairy free
- Freshly ground einkorn flour is whole wheat einkorn flour. If you don't have access to a mill, use strore bought whole wheat einkorn flour.
How to store Einkorn sourdough muffins
Allow the muffins to fully cool and then place in an airtight container or freeze in a plastic bag.
Tips for the Best Muffins

Let muffin batter rise for several hours or overnight
You can bake these right away. The BEST muffins, though are made over time. Allowing the batter to ferment takes advantage of the sourdough starter’s rising power. This will produce the highest muffin tops and most beautiful double chocolate muffins! I recommend several hours to overnight.
Use Mini Chocolate Chips
Mini chocolate chips better spreads the bit’s of melted chocolate throughout the muffin. Though you could use normal size chocolate chips or even chunks, I prefer the small size as it allows more bits of chocolate in each bite.
Bake at high heat
Muffins perform best for a nice rise with sudden high heat temperature. Make sure you bake these at the 450 degrees as listed in the directions.
Do not overmix the batter
These Einkorn muffins are best if the batter is not over mixed. Simply mix until all ingredients are combined.

I’d love to hear how you like these or if you tweak this batter creatively! Let me know.
From the Hilltop,
