Sourdough Vanilla Cupcakes With Fresh Milled Flour (+No Refined Sugar)

Last Updated on April 26, 2026 by Kayla Ruetten

moistbakery-style vanilla cupcake with no sugar or processed flour might be just as exciting as the occasion you’re celebrating!  These sourdough vanilla cupcakes with fresh milled flour make a lightsoft, and a perfect frosted dessert or breakfast on the go. Using only honey for the sweetener, this treat comes together using just one bowl. Try this great starter recipe for learning to bake with sourdough and fresh milled flour. They are simple yet decadent, especially with a cream cheese frosting (also refined sugar free).With just a handful of ingredients, this recipe comes together fast enough for even a week night treat. This recipe can easily become your go-to birthday or after sports game treat cupcake recipe as well.

sourdough vanilla cupcakes with fresh milled flour, topped with whipped cream cheese frosting and dye free sprinkles, presented on a cutting board

New to sourdough or fresh milled flour? These cupcakes are a simple and easy recipe to start with. With staple ingredients, you need no rise time, folds, or yeast. We like to keep our meal system super simple, and this cupcake recipe can be used as a base recipe with different mix in options.. 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 step by step instructions and the detailed recipe card.

FAQ + A Dairy-free Option

  1. Best dye-free sprinkles?
    We love these rainbow ones that are allergen free and do not have dye.
  2. Favorite chlorine-free cupcake liners?
    We use these unbleached, lower-toxin muffin liners. Alternately, grease your muffin pan very well if your do not want to use muffin liners.
    For tulip style cupcake liners, (the taller, bakery style look) I order these natural unbleached ones.
  3. Dairy-free option?
    Yes, you can use different fats or oils in place of the butter in this recipe. We usually use butter or coconut oil.
sourdough vanilla cupcakes with fresh milled flour presented on cutting board topped with whipped cream cheese frosting

Sourdough Vanilla Cupcakes With Fresh Milled Flour

these bakery style sourdough vanilla cupcakes with fresh milled flour come together from bowl to table in 20 minutes. They are sweet, moist, fluffy, and sugar free. Sweetened with honey, they are a healthier baked good, perfect for birthday parties or post sport game celebrations.

Equipment

  • grain mill
  • soft white wheat berries
  • stainless steel muffin tins
  • unbleached muffin/cupcake liners
  • dye free sprinkles (optional)

Ingredients
  

Ingredients for cupcake batter

  • 2.5 cups fresh milled soft white wheat
  • 1 cup honey
  • 1/2 cup sourdough starter
  • 1/2 cup butter (or preferred fat)
  • 1/2 cup water (or milk)
  • 3 eggs
  • 2 tbsp real vanilla extract
  • 1 tsp baking powder
  • 1 tsp baking soda

Ingredients for frosting

  • 8oz block cream cheese
  • 1/2 cup butter, softened
  • 1/4 cup honey

Instructions
 

Instructions for Cupcakes

  • Pre-heat oven to 350 degrees
  • Grind wheat berries. 1 cup of wheat berries yields about 1 and 1/4 to 1 and 1/2 cups of fresh milled flour.
  • Cream together room temperature/softened butter, honey, and vanilla. I like to do this with an immersion blender right in a large glass measuring cup for less dishes. Once creamed, whisk in eggs and sourdough starter.
  • Mix flour, baking powder, and baking soda together in a bowl.
  • Add dry ingredients to wet ingredients and mix until just incorporated. Do not overmix.
  • Add batter to lined or greased muffin instead, filling each muffin holder 3/4 full of batter (about 1/3 cup).
  • Bake at 350 for about 15 minutes or until cupcake is golden brown on the top and bottom. Insert a knife or toothpick into the center of the cupcake. If it comes out clean, the cupcake is done; if it has batter, cook longer and try again in a few minutes.
  • Wait until cupcake is completely cooled before frosting, otherwise the frosting will melt and slide. I pop the cupcakes in the fridge or freezer for a bit to speed the process.

Instructions for Frosting

  • Cream together all ingredients until smooth. I like using an immersion blender best for this but any blender will work.
    Spread on top of room temperature/cooled cake.
    Add sprinkles, if desired.

Notes

We use these unbleached, lower-toxin muffin liners. Alternately, grease your muffin pan very well if your do not want to use muffin liners.
I love our Nutrimill Harvest for grinding grains. 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.
We love these rainbow dye-free sprinkles  that are free of many allergens.

Health Benefits of Fresh Milled Flour & Sourdough

If you have been gluten-free for awhile, due to sensitivities, like our family has, you might be able to successfully introduce fresh milled flour like we have. (Even if sourdough didn’t work for you!)

Why You Will Love These Sourdough Vanilla Cupcakes With Fresh Milled Flour

  1. Taste. The flavor comparison of freshly milled flour to store-bought flour is like a fresh picked apple to a store-bought one. If you’ve been nervous to make the switch, it is so worth it! Enjoy the rich flavors and fluff.
  2. Quick & easy to prepare. You can make this recipe with just a few ingredients and no rise time, folding, or yeast needed.
  3. 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.
  4. Naturally sweetened. This cake and frosting contain no refined sugar, just sweetened with honey, which aids our bodies rather than depletes them.
  5. Simple ingredients. No need for any specialty or unfamiliar ingredients. Just the basics.
sourdough vanilla cupcake with fresh milled flour, cut in half, showing tender crumb and cream cheese whipped frosting

How To Make Sourdough Vanilla Cupcakes With Fresh Milled Flour

You will be delighted how simple these cupcakes are to make!

Ingredients for Cupcake Batter

  • 2.5 cups finely ground fresh milled flour (soft or hard white wheat berries)
  • 1 cup honey
  • 1/2 cup sourdough starter
  • 1/2 cup butter (1 stick)
  • 1/2 cup water
  • 3 eggs
  • 2-3 tablespoons vanilla
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda

Ingredients for Frosting

  • 8 oz block cream cheese
  • 1/2 cup softened/room temperature butter (1 stick)
  • 1/4 cup honey
  • dye-free sprinkles (optionally sprinkled on top)

Instructions for Cake

  • Preheat oven to 350 degrees.
  • Grind wheat berries. 1 cup of wheat berries yields about 1 and 1/4 to 1 and 1/2 cups of fresh milled flour.
  • Cream together room temperature/softened butter, honey, and vanilla. I like to do this with an immersion blender right in a large glass measuring cup for less dishes. Once creamed, whisk in eggs and sourdough starter.
  • Mix flour, baking powder, and baking soda together in a bowl.
  • Add dry ingredients to wet ingredients and mix until just incorporated. Do not overmix.
  • Pour batter into lined cupcake/muffin tins. Use these liners for unbleached/non chlorinated option. Gently tap the dish against the counter to remove air pockets.
  • Bake at 325 for about 15 minutes or until cupcakes are golden brown on the top and bottom. Insert a knife or toothpick into the center of the cupcake. If it comes out clean, the cupcake is done; if it has batter, cook longer and try again in a few minutes.
  • Wait until cupcakes are completely cooled before frosting, otherwise the frosting will melt and slide. I pop the cupcakes in the fridge or freezer for a bit to speed the process.

Instructions for Frosting

  • Cream together all ingredients until smooth. I like using an immersion blender best for this but any blender will work.
  • Spread on top of room temperature/cooled cupcakes.

Gluten Sensitivity

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. We, like many others, tried from scratch sourdough first, using store-bought flour. We continued to have inflammatory reactions from this. Now we make our sourdough and starter using only fresh milled grains and this has made all the difference for us. We have also, remarkably, been able to consume straight fresh mill flour baked goods (not fermented with sourdough first) without reactions since. Disclaimer: I am not a medical doctor, and this is not medical advice. If you have celiac or food allergies, talk with your doctor before adding in any new foods including this recipe.

Check out the process we used to heal from food allergies, auto-immune, and eczema here.

We hope your family enjoys these fun sourdough vanilla cupcakes with fresh milled flour as much as ours does! We would love your feedback in the comments below.

sourdough fresh milled flour cupcakes with cream cheese frosting presented on cutting board

Resources

More Sourdough and Fresh Milled Flour Recipes

Fresh Milled Flour Sourdough Crackers
Flaky Fresh Milled Flour Biscuits (Dairy-Free Option!)
Fresh Milled Flour Sourdough Pancakes (Dairy-Free Option!)
Fresh Milled Flour Tortillas-4 Ingredients

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