Whole Wheat Blueberry Muffins with Freshly Milled Flour

Name: Whole Wheat Blueberry Muffins with Freshly Milled Flour
Prep time: 15 min
Cook time: 25 min
Total time: 40 min
Ingredients: 2 cups fresh milled soft white wheat (280 grams); 1 cup sugar (192 grams); 2 teaspoons baking powder (8 grams); ½ teaspoons salt (3 grams); 2 eggs; ½ cup butter melted (113 grams); 1 teaspoon vanilla (5 grams); ¼ cup milk (61 grams); 1 cup blueberries; ¼ cup soft white wheat flour (35 grams); 1 tablespoon brown sugar (13 grams); 1 tablespoons sugar (12 grams); ¼ teaspoon cinnamon; Pinch of salt; 2 tablespoons cold butter (28 grams)

By Lisa Bass

on Mar 23, 2026

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Whole wheat blueberry muffins are a perfect treat for busy mornings. These fluffy muffins are made with juicy blueberries, freshly milled flour and baked until golden brown with an irresistible crunchy topping.

one blueberry muffin on a blue decorative plate with 3 blueberries beside it.

Why You’ll Love This Recipe
Ingredients
Tools You May Need
How to Make Whole Wheat Blueberry Muffins
Tips
Recipe FAQs
More Freshly Milled Recipes from the Farmhouse
Whole Wheat Blueberry Muffins with Freshly Milled Flour Recipe

Homemade muffins are something we whip up on a regular basis around here. They are just so easy to make and perfect for any time of day. Some of our favorites to keep on rotation are lemon poppyseed muffins, morning glory muffins, chocolate einkorn protein muffins and these delicious whole wheat blueberry muffins!

This recipe is a delicious take on a classic blueberry muffin (check out my sourdough blueberry muffin recipe here) but with the healthy addition of using freshly milled flour which is packed with vitamins and minerals, and great for easier digestibility. It is a perfect treat to enjoy for breakfast with sunny side up eggs or as a simple afternoon treat with a warm cup of coffee or lavender latte.

Why You’ll Love This Recipe

Wholesome – This healthy blueberry muffin recipe is made with simple ingredients and nutrient dense freshly milled flour, making it a great wholesome treat to whip up and enjoy.

Fresh blueberry flavor – The fresh taste of blueberry in these delicious little morsels are reminiscent of our favorite spring and summer flavors.

Versatile snack – These are the best muffins, perfect for quick breakfasts, school lunches, afternoon snacks and even a little sweet treat to end a long day.

Ingredients

Freshly milled soft white wheat – Soft white wheat is best for a softer crumb. Store bought whole wheat flour also works well.

Vanilla – Homemade vanilla extract is easy to make and elevates any baked good recipe.

Blueberries – You can use fresh or frozen blueberries for these whole-wheat blueberry muffins. Frozen berries bleed into the batter more than fresh berries, but either work beautifully. Do not thaw frozen berries before incorporating them into the batter.

A full ingredient list with exact amounts can be found in the recipe card below.

Tools You May Need

Mockmill – Read my review on the Mockmill versus Nutrimill for more information on why I chose this specific mill.

How to Make Whole Wheat Blueberry Muffins

butter, flour, cinnamon, and sugar mixed together on a white plate to make a crumble.

Step 1: Preheat oven temperature to 375 degrees F. Mix together streusel topping using a pastry cutter, a fork, or your fingers until the butter is broken into dime size pieces and everything is combined. Set aside.

flour, salt, and baking powder whisked together in a glass bowl.

Step 2: In a large bowl, mix together flour, sugar, baking powder and salt.

butter, eggs, and sugar mixed together in a glass bowl.

Step 3: In a separate small bowl, add eggs, melted butter, vanilla and milk, and whisk until well combined.

dry muffin ingredients mixed with wet muffin ingredients.

Step 4: Combine the wet ingredients with the dry ingredients and carefully mix just until no dry streaks remain. Be careful not to over mix.

Step 5: Fold in the blueberries.

Step 6: Scoop the muffin batter into a prepared muffin tin, about ⅔ of the way full.

streusel topping sprinkled over blueberry muffin batter in the muffin tin.

Step 7: Divide the streusel evenly among the tops of the muffins.

twelve blueberries muffins cooling on a wire wrack.

Step 8: Bake the muffins for 22-25 minutes. Then, transfer the muffins to a wire cooling rack to cool slightly. Serve and enjoy!

one whole wheat blueberry muffin on a blue decorative plate with a cooling wrack full of muffins in the background.

Tips

If you are using freshly milled grains for this recipe, I recommend weighing the flour instead of using volume measurements. Grain mills vary greatly – some create very fine and fluffy flour, while others are a little more coarse. This makes volume measurements unpredictable. Using a kitchen scale and calculating the grams is much more reliable, ensuring you end up with a delicious end product.
Be sure not over mix the batter while making muffins to achieve the best results and avoid a dense end result.
Fold the blueberries in gently to keep them from bursting in the batter.

Recipe FAQs

What happens if you use whole wheat flour instead of all-purpose flour?

Whole wheat flour gives you a texture that is a bit heavier and more dense than all purpose white flour. There is also a distinct nutty flavor that comes with baking with whole wheat flour.

Are whole wheat muffins actually healthy?

Freshly milled whole-wheat flour keeps the bran and germ of the wheat berry intact which is nutrient dense and filled with vitamins, minerals, fiber and healthy fats. Using whole wheat flour is a great swap to make from baking with all purpose flour.

What is one thing you should never do to a muffin mixture?

The number one thing to avoid when making this whole wheat muffin recipe is over mixing the batter. This will leave you with dense and heavy muffins rather than a light and airy crumb.