Sourdough Fresh Milled Flour Muffins – No Sugar
Last Updated on March 31, 2026 by Kayla Ruetten
If you want the best taste of fresh fresh milled flour plus asuper easy beginner muffin, this recipe is for you. These sourdough fresh milled flour muffins have just a handful of ingredients and no refined sugar. They come together quickly for breakfast or dessert. Everyone who has tried these loves the fluffy, moist and bakery fresh taste. I try to bake enough of these to eat fresh plus freeze for quick snacks to pull from later. I love using sourdough starter for added gut health, and this recipe uses a good amount of it.

New to fresh milled flour? These muffins are a simple and easy recipe to start with. With simple ingredients, you need no rise time, folds, or yeast. We like to keep our meal system super simple, and this muffin recipe can be used as a base recipe with different mix in options, such as nuts and dried fruits. As a bonus, they freeze and thaw very well; perfect for busy families.
This easy, same day sourdough fresh milled dessert can be used with active starter or discard and pulls together from ingredients to the table in just 20 minutes! More beginner fresh milled flour & sourdough recipes here.
Scroll down for the detailed recipe card.
Helpful Resources to Make This Recipe
Sourdough Fresh Milled Flour Muffins – No Sugar

Ingredients
- 2 cups finely ground fresh milled flour (I used soft white wheat)
- 1 cup water
- 1 cup chocolate chips (or other mix ins)
- 1/2 cup honey
- 1/2 cup active sourdough starter
- 1/3 cup melted coconut oil
- 1 egg
- 1 teaspoon baking powder
- 1 teaspoon baking soda
Instructions
- Grind wheat berries. 1 cup of wheat berries yields about 1 and 1/4 to 1 and 1/2 cups of fresh milled flour.
- Mix wet ingredients together in a mixing bowl.
- Then add baking powder, salt, and flour and mix together.
- Fold in chocolate chips or other mix ins.
- Allow dough to rest for 30 minutes
- Add dough to lined or greased muffin instead, filling each muffin holder 3/4 full of batter (about 1/3 cup).
- Bake at 400 degrees for about 15 minutes until muffins are golden brown and cooked through the middle. (Insert a knife or toothpick. When it comes out clean, the batter is fully cooked).
- Store at room temperature or in the fridge for 2-3 days or freeze for 2-3 months.
FAQ
- Is it ok to substitute butter or lard in this recipe?
Yes, you can use lard or butter in this recipe in place of the coconut oil. - What kind of muffin liners do you use?
We use these unbleached, lower-toxin muffin liners. Alternately, grease your muffin pan very well if your do not want to use muffin liners. - Do these muffins freeze and thaw well?
Yes! We have had great results with freezing and thawing. - What grain mill do you recommend?
I love our Nutrimill Harvest. It grinds course to fine and leaves very little flour dust compared to other mills. I love that it looks beautiful on the countertop as well! Use GROWINGTHROUGHGAPS code at checkout for discount.
Why You Will Love Sourdough Fresh Milled Flour Muffins
- Taste. The flavor comparison of freshly milled flour to store-bought flour is so fresh! The smell and taste are just so much more “grain-forward”.
- Quick & easy to prepare. You can make this recipe with just a few ingredients and no rise time, folding, or yeast needed.
- Healing diet friendly. This recipe has fresh milled flour, which is completely different than using store-bought flour. It is lightyears healthier and less inflammatory than even from scratch sourdough using store-bought flour. Whether you are eating GAPS, Paleo, whole food, or just becoming more ingredient aware, this recipe is can be a compatible next step following many healing diets.
- Versatile. You can use this recipe for a base muffin recipe, switching out your mix-ins, like nuts and dried fruits.
- Simple ingredients. No need for any specialty or unfamiliar ingredients. Just the basics.
Gluten Sensitivity
Why are so many of us sensitive to gluten? Is it actually the gluten? Or is it modern flour, processed and stripped of nutrients? Perhaps a combination of processed flour + the poor immune and digestive system so many of us and/or our children seem to have. It has become so common to have allergies, asthma, or some sort of auto-immune condition that it doesn’t seem abnormal. It is not normal, just because it is common. As our family healed from food allergies using a gut healing protocol, we learned how to re-create favorite recipes with healthier alternatives. With myself and all our children being gluten-sensitive, we were so thrilled to discover we tolerate fresh milled flour well. Check out the process we used to heal from food allergies, auto-immune, and eczema here.
We hope your family enjoys these soft, fresh milled flour sourdough chocolate chip muffins as much as ours does! We would love your feedback in the comments below.
Sourdough Fresh Milled Flour Muffins – No Sugar
Equipment
- flour mill
- wheat berries (I used soft white)
- stainless steel muffin tins
- unbleached, lower toxin muffin liners
- coconut oil
- honey
- chocolate chips or other mix ins
- baking soda
- baking powder
Ingredients
- 2 cups finely ground fresh milled flour (I used soft white wheat)
- 1 cup water
- 2/3 cup melted coconut oil
- 1/2 cup sourdough starter
- 1/2 cup honey
- 1 egg
- 1 tsp baking soda
- 1 tsp baking powder
- 1 cup chocolate chips (or other favorite mix ins)
Instructions
- Grind wheat berries. 1 cup of wheat berries yields about 1 and 1/4 to 1 and 1/2 cups of fresh milled flour.
- Mix wet ingredients together; then add dry ingredients (minus chocolate chips) and mix.
- Fold in chocolate chips or other mix-ins.
- Allow dough to rest for 30 minutes, then add dough to lined or greased muffin pans, filling each muffin holder 3/4 full of batter.
- Bake at 350 degrees for about 20 minutes until muffins are golden brown and cooked through the middle. (Insert a knife or toothpick. When it comes out clean, the batter is fully cooked).
- Store at room temperature or in the fridge for 2-3 days or freeze for 2-3 months.
Resources
More Beginner Fresh Milled & Sourdough Recipes
Fresh Milled Flour Blueberry Muffins – No Sugar
Fresh Milled Flour Sourdough Crackers
Flaky Fresh Milled Flour Biscuits (Dairy-Free Option!)
Fresh Milled Flour Sourdough Pancakes (Dairy-Free Option)
Fresh Milled Flour Sourdough Vanilla Cake (No Refined Sugar)
Fresh Milled Flour Tortillas (Without Sourdough Starter)
Posts
Fresh Milled Flour & Sourdough
What is the GAPS Diet – An Easier Explanation
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