Sourdough Blueberry Muffins With Fresh Milled Flour
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These whole wheat sourdough blueberry muffins made with freshly milled flour are soft, light, and packed with natural sweetness, making them the perfect breakfast or snack.

Adding freshly milled flour into a typical blueberry muffin, you get something that not only is bursting with flavor, but is also full of wholesome nutrition.
If you are totally new to freshly milled grains, make sure to check out my guide on how to mill flour at home.
This is a great recipe to start with. It’s very simple and can be made quickly or long fermented for more health benefits. These tasty muffins make the perfect snack, breakfast, or dessert.
My kids love them for breakfast (or we make toast with the best whole wheat sourdough sandwich bread). We pop already baked muffins in the oven in the morning to warm up and serve them with some farm fresh eggs or bacon.
Recipe Highlights
- Nutrient-packed: The freshly milled flour retains all the goodness of the whole grain, providing more fiber, vitamins, and minerals than traditional store-bought flour. You’re not just enjoying a delicious muffin; you’re also giving your body the nourishment it needs.
- Tangy and sweet: The sourdough starter adds a subtle tang that balances perfectly with the natural sweetness of blueberries, creating a muffin that’s rich in flavor without being overly sweet.
- Perfectly moist: Freshly milled flour helps to keep the muffins moist while providing a hearty, satisfying texture. No dry, crumbly muffins here!
- Customizable: Feel free to swap in different fruits (like raspberries or blackberries) or add-ins (like nuts or chocolate chips) for your own spin on this recipe.
Ingredients Needed

Sourdough starter: Active or discard will work.
Fresh milled flour: I like to use soft white wheat berries. This type of wheat works well due to it’s lower protein and gluten content, giving it a softer crumb.
Blueberries: Fresh or frozen.
Sugar: You could also omit the milk or water and use maple syrup or honey.
Find the rest of the ingredients needed in the recipe card below.
Tools
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Grain mill: I have a Mockmill. You can find my best grain mill comparison here.
How to Make Whole Wheat Sourdough Blueberry Muffins with Freshly Milled Flour

Step 1: Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or grease it lightly to prevent sticking. Mill your soft white wheat.

Step 2: In a large bowl or a bowl of a stand mixer with a paddle attachment, whisk the sourdough starter, milk, melted butter, eggs, honey, and vanilla extract until smooth.

Step 3: In a separate bowl, mix the freshly milled flour, baking powder, baking soda, salt, and cinnamon (if using). Make sure to whisk the dry ingredients well to ensure an even distribution of the leavening agents.

Step 4: Add the dry ingredients to the wet ingredients and gently fold until just combined. Be careful not to over-mix. Over mixing can lead to dense muffins. It’s okay if there are a few lumps. Fold in the blueberries gently.

Step 5: Using a spoon or ice cream scoop, divide the batter evenly into the muffin tin, filling each cup about 3/4 full. If desired, sprinkle a little sugar on top for a crunchy topping.

Step 6: Bake the muffins in the preheated oven for 18–22 minutes or until a toothpick inserted into the center comes out clean or with just a few crumbs attached. The tops should be golden and slightly domed.

Step 7: Let the muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely. Serve them warm for the best flavor and texture.
Tips for Success
- If you’re new to freshly milled flour, note that it can be a bit more absorbent than store-bought flour. If your batter seems too thick, add a little more milk, a teaspoon at a time, until you reach the desired consistency.
- When adding blueberries to your muffin batter, dust them lightly in flour before folding them in. This can help prevent them from sinking to the bottom during baking. Also, before folding the blueberries into the batter, scoop a little plain batter into the bottom of the muffin tin, then fold in the blueberries to the remaining batter and fill the muffin tin with remaining batter.
- These muffins can be stored at room temperature in an airtight container for 2–3 days, or you can freeze them for up to 3 months. To freeze, place them in a freezer bag and store for up 3 months or more.
- If you’re using frozen blueberries, don’t thaw them before adding them to the batter, as this can cause the batter to become too wet and result in a streaky color.
Variations
- Lemon Blueberry Muffins: Add the zest of one lemon to the batter for a fresh, citrusy twist. The tang of the lemon pairs wonderfully with the sourdough starter and blueberries.
- Oatmeal Blueberry Muffins: Stir in 1/2 cup of rolled oats for extra texture and fiber. You can also sprinkle some oats on top before baking for a rustic look.
- Chia or Flax Seeds: For added nutrition, add a tablespoon of chia seeds or ground flaxseed to the batter. These healthy seeds provide healthy fats, fiber, and omega-3s.
- Nuts: Add a little extra crunch with chopped pecans, walnuts, or whatever nuts you prefer.
FAQ
Yes, you can use all-purpose flour or whole wheat flour from the store. However, freshly milled flour provides a richer flavor and more nutrients, so we highly recommend it if you can. If using all-purpose, you may not want to add as much milk or water compared to whole wheat.
While the sourdough starter adds a unique tang and helps with leavening, you can substitute it with 1/2 cup of buttermilk or plain yogurt if you prefer. This will change the flavor slightly but still yield a delicious muffin.
Yes, frozen blueberries work well in this recipe. Just add them directly to the batter without thawing them to prevent excess moisture from being released into the muffin batter.
Find more sourdough recipes:
- Sourdough Apple Crisp
- Sourdough Pumpkin Muffins
- Easy Sourdough Blueberry Scones
- Sourdough Discard Bread
- Whole Wheat Sourdough Pizza Dough With Fresh Milled Flour
If you try this recipe and love it, I would love if you could come back, comment on the post, and give it 5 stars! Please and thank you. Tag me on Instagram @ablossominglife

Sourdough Blueberry Muffins With Fresh Milled Flour
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Equipment
- Muffin pan
Ingredients
- 1/2 cup sourdough starter active or discard
- 1 1/2 cups whole wheat flour fresh milled soft white wheat
- 1/3 cup butter melted- or oil
- 3/4 cup sugar
- 1/4 cup milk or water
- 2 large eggs
- 1/2 teaspoon baking soda
- 1/4 teaspoon baking powder
- 1/4 teaspoon salt
- 1 teaspoon vanilla extract
- 1 teaspoon flour optional
- 1 cup blueberries fresh or frozen – add a little more if desired
Instructions
- Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or grease it lightly to prevent sticking.
- In a large bowl or a bowl of a stand mixer with a paddle attachment, whisk the sourdough starter, milk, melted butter, eggs, honey, and vanilla extract until smooth.
- In a separate bowl, mix the freshly milled flour, baking powder, baking soda, salt, and cinnamon (if using). Make sure to whisk the dry ingredients well to ensure an even distribution of the leavening agents.
- Add the dry ingredients to the wet ingredients and gently fold until just combined. Be careful not to overmix—overmixing can lead to dense muffins. It’s okay if there are a few lumps.
- Fold in the blueberries gently. If you’re using frozen blueberries, don’t thaw them before adding them to the batter, as this can cause the batter to become too wet and result in a streaky color.
- Using a spoon or ice cream scoop, divide the batter evenly into the muffin tin, filling each cup about 3/4 full. If desired, sprinkle a little sugar on top for a crunchy topping.
- Bake the muffins in the preheated oven for 18–22 minutes or until a toothpick inserted into the center comes out clean or with just a few crumbs attached. The tops should be golden and slightly domed.
- Let the muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely. Serve them warm for the best flavor and texture.
Notes
- If you’re new to freshly milled flour, note that it can be a bit more absorbent than store-bought flour. If your batter seems too thick, add a little more milk, a teaspoon at a time, until you reach the desired consistency.
- When adding blueberries to your muffin batter, dust them lightly in flour before folding them in. This can help prevent them from sinking to the bottom during baking. Also, before folding the blueberries into the batter, scoop a little plain batter into the bottom of the muffin tin, then fold in the blueberries to the remaining batter and fill the muffin tin with remaining batter.
- These muffins can be stored at room temperature in an airtight container for 2–3 days, or you can freeze them for up to 3 months. To freeze, place them in a freezer bag and store for up 3 months or more.

