Fresh Milled Flour Recipe Blueberry Lemon Muffins
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The best fresh milled flour recipe blueberry lemon muffins. These delicious and healthy bakery-style muffins are a breeze to make at home!

Blueberry and lemon are one of my favorite muffin flavor combinations. The sweetness of blueberries and the tang of lemon flavor always hits the spot. Add a little crumb topping or creamy lemon glaze and then I’m really in heaven!
This recipe for homemade muffins is the natural result of my love for both. These are the best lemon-blueberry muffins I’ve ever had and they’re also healthy with fresh milled whole grain flour. Obsessed is most definitely the right word!
If you want to try fabulous and healthy bakery-style muffins with the fresh ingredients, perfect texture and amazing flavor, this is your recipe!


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Fresh Milled Flour Makes the Best Muffins
If you know me, you’ll know I love freshly milled flours. I mill all of my flour from wheat berries. It’s a quick and easy process that you can read about in how to mill your own flour and the health benefits.
Fresh milled flour is the best kept secret in baking. In a nutshell, you get the best flavor and the most nutrients from your flours within the first hours and days after they are milled. Quality declines significantly after that.
You have no way of knowing how long a bag of flour has been sitting on your grocery store shelf. That’s why I use fresh milled flour for muffins and everything else. It’s top quality every time!


For tips on how to get perfect muffins every time, checkout my muffin making tips.
Now, let’s get started!
Blueberry Lemon Muffin Recipe Ingredients
Wet Ingredients
- 3/4 cup plain yogurt
- 2 eggs
- ½ cup honey
- ½ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
- 1 teaspoon pure vanilla extract
- Zest of 1 large lemon (about 1 tablespoon)
- 2 tablespoons fresh lemon juice
Dry Ingredients
- 2 cups (260 grams) freshly milled flour
- 1 teaspoon salt
- 1 teaspoon baking powder
- 3/4 teaspoon baking soda
Mix-Ins
- 1 cup fresh or frozen blueberries (or any berry, just do NOT let the frozen berries thaw before mixing)
- 1 tablespoon freshly milled flour (to toss berries)


Optional Toppings
Lemon Crumb Topping
- ⅓ cup (40 grams) freshly milled flour
- 2 tablespoons cane sugar
- 1 teaspoon lemon zest
- 2 tablespoons melted butter


Creamy Lemon Glaze
- ½ cup plain yogurt
- 1 tablespoon lemon zest
- 1 tablespoon fresh lemon juice
- 1-2 tablespoons pure maple syrup or honey
How to Make Lemon Blueberry Muffins
Preheat your oven to 425°F (220°C). Grease a muffin tin and set aside.
In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.
Add the freshly milled flour and salt to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.


While resting the batter, make the lemon crumb (if desired) by combining the flour, sugar, zest, and melted butter in a small bowl. Use a fork or your fingers to bring it together into a dry, crumbly mixture. If it is more pasty than crumbly, add more flour. Set aside.
After resting, add the baking powder and baking soda to the muffin batter. Mix gently until everything is evenly combined, being careful not to overmix.
Toss the blueberries in the tablespoon of flour, until coated. This will help prevent the berries from sinking to the bottom. Fold the floured blueberries into the batter.


Working quickly, spoon the batter into the prepared muffin pan, filling each cup evenly.
If adding the lemon crumb topping, sprinkle the prepared topping over each muffin, gently pressing the crumbs into the batter.
Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 10-12 minutes, or until the centers feel firm and the muffins are baked through.
Remove from the oven and let cool slightly on a wire rack.
While cooling, prepare the lemon glaze by combining the yogurt, zest, lemon juice and sweetener of choice. Right before serving, drizzle the glaze over the top of each muffin. Enjoy!
Printable Blueberry Lemon Muffins Recipe Card


Blueberry Lemon Muffins with Fresh Milled Flour
An unbeatably delicious recipe blueberry lemon muffins made with freshly milled flour. Try it with a crumb topping or sweet lemon glaze. This is a must-have recipe!
Wet Ingredients
- 3/4 cup plain yogurt
- 2 eggs
- ½ cup honey
- ½ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
- 1 teaspoon pure vanilla extract
- Zest of 1 large lemon (about 1 tablespoon)
- 2 tablespoons fresh lemon juice
Dry Ingredients
- 2 cups (260 grams) freshly milled flour
- 1 teaspoon salt
- 1 teaspoon baking powder
- 3/4 teaspoon baking soda
Mix-Ins
- 1 cup fresh or frozen blueberries (or any berry, just do NOT let the frozen berries thaw before mixing)
- 1 tablespoon freshly milled flour (to toss berries)
Lemon Crumb Topping (Optional)
- ⅓ cup (40 grams) freshly milled flour
- 2 tablespoons cane sugar
- 1 teaspoon lemon zest
- 2 tablespoons melted butter
Creamy Lemon Glaze (Optional)
- ½ cup plain yogurt
- 1 tablespoon lemon zest
- 1 tablespoon fresh lemon juice
- 1-2 tablespoons pure maple syrup or honey
-
Preheat your oven to 425°F (220°C). Grease a muffin tin and set aside.
-
In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.
-
Add the freshly milled flour and salt to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.
-
While resting the batter, make the lemon crumb (if desired) by combining the flour, sugar, zest, and melted butter. Use a fork or your fingers to bring it together into a dry, crumbly mixture. If it is more pasty than crumbly, add more flour. Set aside.
-
After resting, add the baking powder and baking soda to the muffin batter. Mix gently until everything is evenly combined, being careful not to overmix.
-
Toss the blueberries in the tablespoon of flour, until coated. This will help prevent the berries from sinking to the bottom. Fold the floured blueberries into the batter.
-
Working quickly, spoon the batter into the prepared muffin tin, filling each cup evenly.
-
If adding the lemon crumb topping, sprinkle the prepared topping over each muffin, gently pressing the crumbs into the batter.
-
Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 10-12 minutes, or until the centers feel firm and the muffins are baked through.
-
Remove from the oven and let cool slightly on a wire rack.
-
While cooling, prepare the lemon glaze by combining the yogurt, zest, lemon juice and sweetener of choice. Right before serving, drizzle the glaze over the muffins.
-
Store cooled muffins in an airtight container at room temperature for up to 2 days. For longer storage, freeze the muffins the same day they’re baked. Thaw at room temperature before serving.
Storing Blueberry Lemon Muffins
Store cooled muffins in an airtight container at room temperature for up to 2 days.
For longer storage, wrap the muffins and place in a freezer safe container or bag the same day that they’re baked. Store for up to a few weeks. Thaw at room temperature before serving.


Where to Get Baking Supplies
If you need baking supplies, checkout the Bread Making Supplies page. It’s where I share information and links to all my baking favorites. Only the best products make in onto this page!
More Recipes Like This
Lemon blueberry muffins made with fresh milled flour make a terrific breakfast or snack! These babies have perfect flavor, moisture and texture. Good enough to rival any bakery muffin I’ve ever tried, and I haven’t even mentioned how incredibly healthy they are!
Grab your ingredients and try these today!


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