Fresh-Milled Double Chocolate Muffins (Soft White Wheat, Whole Grain)
Last Updated on January 27, 2026 by Stephanie Gilpin
If you love chocolate, these double chocolate muffins are about to become a fresh-milled flour staple in your kitchen.
They’re rich, moist, and full of melty chocolate chips, but thanks to soft white wheat flour, they still offer whole-grain fiber and protein that give them more staying power than a typical bakery muffin.
These muffins bake up tall and tender with deep chocolate flavor. They make a great after-school snack or a “healthier” dessert, and paired with eggs or yogurt, they work well as a balanced yet indulgent breakfast too.
For beginners just getting started with fresh-milled flour, I have a full guide that walks you through the basics and shares beginner-friendly recipes so you can experience quick, easy wins.
Why These Whole Grain Muffins Work
- Made with freshly milled soft white wheat (full of satisfying nutrition)
- Deep chocolate flavor from cocoa and chocolate chips
- Soft, fluffy interior
- Quick, easy to make recipe
- Higher fiber and protein than standard chocolate muffins
If you enjoy fresh-milled flour baking, make sure to try my Blueberry Muffins with Fresh-Milled Flour or my Banana Bread with Fresh-Milled Flour next.
Ingredients
Dry Ingredients
- 2 1/4 cups fresh-milled soft white wheat flour (mill about 1 2/3 cups soft wheat berries)
- 1 1/2 teaspoons baking powder
- 1/2 teaspoons baking soda
- 1/2 teaspoon salt
- 1/2 cup cocoa powder
- 1 1/4 cups semi-sweet chocolate chips
Wet Ingredients
- 3/4 cup melted butter
- 3/4 cup white sugar
- 2 eggs
- 1/4 cup sour cream or Greek yogurt
- 1 cup whole milk
- 1 teaspoon vanilla extract
Instructions
- Preheat the oven to 400°F and line a 12-cup muffin tin with paper liners.
- In a large bowl, whisk together the melted butter, sugar, eggs, Greek yogurt (or sour cream), milk, and vanilla.
- In a separate bowl, whisk the flour, baking powder, salt, and cocoa powder.
4. Add the dry ingredients to the wet ingredients and stir gently until just combined. Do not overmix.
5. Let the batter rest for 10 to 15 minutes to allow the fresh-milled flour to hydrate. Do NOT skip this step!
6. Fold in the chocolate chips.
7. Divide the batter between the 12 muffin cups. They will be full.
8. Bake for 15 to 18 minutes, or until a toothpick comes out clean or with moist crumbs.
9. Cool slightly before serving.
Nutrition Information
These muffins contain approximately:
- 8 grams of protein
- 6.9 grams of fiber
They are slightly higher in sugar than my blueberry muffins due to the chocolate chips, but still offer significantly more nutrition than a standard chocolate muffin.
Double Chocolate Muffins with Fresh-Milled Flour (Soft White Wheat)
Ingredients
Ingredients
Dry Ingredients:
- 2 1/4 cups fresh-milled soft white wheat flour
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 1/2 cup cocoa powder
Wet Ingredients:
- 3/4 cup melted butter
- 3/4 cup white sugar
- 2 eggs
- 1/4 cup sour cream or Greek yogurt
- 1 cup whole milk
- 1 teaspoon vanilla extract
- 1 1/4 cups semi-sweet chocolate chips
Instructions
Instructions
- Preheat oven to 400°F. Line a 12-cup muffin tin with paper liners.
- In a large bowl, whisk together the melted butter, sugar, eggs, Greek yogurt (or sour cream), milk, and vanilla until smooth.
- In a separate bowl, whisk the fresh-milled flour, baking powder, baking soda, salt, and cocoa powder.
- Add the dry ingredients to the wet ingredients and stir gently until just combined. Do not overmix.
- Let the batter rest for 10–15 minutes to allow the fresh-milled flour to hydrate and soften.
- Fold in the chocolate chips.
- Divide the batter evenly among the 12 muffin cups. They will be full.
- Bake for 15–18 minutes, or until a toothpick inserted in the center comes out clean or with moist crumbs.
- Cool slightly before serving.
Notes
- Resting the batter is important for soft texture when using fresh milled flour.
- Each muffin contains approximately 8 grams of protein and 6.9 grams of fiber.
- Mini chocolate chips can be used for more even distribution.
- For more whole-grain recipes, see my Fresh-Milled Flour Baking Guide.
What to Bake Next
If you enjoy baking with fresh-milled flour, try my Blueberry Muffins with Fresh-Milled Flour or Banana Bread with Fresh-Milled Flour. For something savory, my Honey Wheat Sandwich Bread is a great everyday loaf!
