Whole Wheat Fudgy Brownies Recipe – Soft, Chewy, and Naturally Rich
If you’re craving a rich, chocolatey treat but want something a little more wholesome, these whole wheat fudgy brownies are the answer. Made with finely milled whole wheat flour, this easy brownie recipe delivers all the soft, chewy texture and deep cocoa flavor you love—without sacrificing nutrition. Whether you’re baking for a crowd, treating your family, or just indulging in a better-for-you dessert, these healthier brownies are a delicious way to enjoy something sweet while still using whole grains. Best of all, no one will ever guess they’re made with whole wheat!

Why You Will LOVE these Whole Wheat Fudgy Brownies
If you love thick, chewy brownies with rich chocolate flavor, this recipe is for you my friend! Made with freshly milled whole wheat flour, these brownies offer a wholesome twist without sacrificing the decadence you expect from a classic dessert. Perfect for a weeknight treat, bake sale, or just because—you’ll be wanting to make these over and over again!
Ingredients You Will Need For This Recipe
- Milled Whole Wheat Flour- I used Soft White Wheat Berries
- Eggs
- Dutch Cocoa Powder
- Butter
- Granulated Sugar
- Brown Sugar
- Salt
- Vanilla Extract
- Optional: Expresso powder, chocolate chips, nuts, dried fruit

What Makes These Brownies Healthier?
Using whole wheat flour in place of all-purpose adds more fiber, nutrients, and a slightly nutty flavor that complements the chocolate. This recipe proves you don’t need refined flour to make a dessert that’s still indulgent.
Tips To Give Your Brownies The Perfect Fudgy Texture
- Use room temperature eggs for the best texture
- Do not overmix the batter- Mix until just combined for best results
- Slightly under bake the brownies to help lock in the moisture for optimal gooeyness
- Allow to cool completely before cutting ( I KNOW…impossible right?)
How to Make Whole Wheat Brownies (Step-by-Step)
- Preheat oven to 350 degrees and line/spray a 9×9 baking pan
- Mill your flour and and add to a medium bowl
- Next, add in cocoa powder and salt, set aside.
- Melt the butter in a small bowl in the microwave or in a small sauce pan on the stove
- In a stand mixer or medium mixing bowl, whip the eggs and sugars until they reach the “ribbon stage” or until fluffy. This helps to give the whole wheat brownies that nice crackling top! *If using a stand mixer for this stage, I recommend mixing on speed 6 for about 90 seconds.
- Add in vanilla and melted butter. Mix until combined.
- Now, slowly add in your flour mixture and fold until just combined. Do not overmix!
- Pour into prepared pan and bake for about 30-35 minutes or until the brownies are just set to touch. They will continue to cook as they cool. You don’t want it to be jiggly, just set to touch.
- Remove the pan from the over and allow the whole wheat fudgy brownies to cool on a cooling rack before cutting.
- Cut and serve. Enjoy!
Helpful Tip: If you want even fudgier brownies add a handful of chocolate chips to the batter right before baking!
Whole Wheat vs All-Purpose Flour
Whole wheat flour brings depth and richness with added nutrients, while all-purpose flour tends to yield a fluffier texture. In this recipe, the whole wheat version keeps things fudgy without tasting too “healthy.” It’s the best of both worlds.

Serving Ideas and Flavorful Add-Ins
Try these delicious brownie add-ins and variations:
- Chopped Walnuts or Pecans
- Swirl in peanut butter, almond butter, or cream cheese
- top with flaky sea salt or dust with cocoa powder and powder sugar
- add dark chocolate chips or M&Ms
- Mix in freeze dried fruits
To serve:
- Add a scoop of vanilla ice cream on top
- Drizzle chocolate syrup or caramel
- serve with your favorite fruit like fresh raspberries or strawberries

FAQs
Can I substitute whole wheat flour in any brownie recipe?
Yes, but you may need to slightly reduce the amount. This recipe is tested with 100% whole wheat for the perfect texture.
Do whole wheat brownies taste different?
They have a slightly nuttier flavor but are still rich, sweet, and chocolatey.
Can I make these dairy-free?
Yes! Substitute coconut oil for butter and use dairy-free chocolate chips.
How to Store and Freeze Whole Wheat Fudgy Brownies
Keep in an airtight container for up to 4 days. You may also freeze these brownies for up to three months-although I seriously doubt they will not be gone before then!

Enjoy these other dessert recipes:
Sourdough Pumpkin Muffins Made with Freshly Milled Grains
Quick Made From Scratch Sourdough Banana Bread
The Only Chocolate Chip Cookie Recipe You’ll Ever Need
Quick Sourdough Discard Cinnamon Rolls
SWEET AND SALTY CHRISTMAS CANDY

Whole Wheat Fudgy Brownies Recipe
Ingredients
- 192 grams Freshly Milled Soft White Wheat Flour It is about 1 3/4 cup
- 1 cup Butter, Melted
- 3 Eggs
- 1 cup Granulated Sugar
- 1 cup Brown Sugar
- 3/4 cup Dutch Cocoa Powder
- 1 tsp Salt
- 2 tsp Vanilla Extract
- Mix-Ins of Choice
Instructions
- Preheat oven to 350 degrees and line/spray a 9×9 baking pan
- Mill your flour and and add to a medium bowl
- Next, add in cocoa powder and salt, set aside.
- Melt the butter in a small bowl in the microwave or in a small sauce pan on the stove
- In a stand mixer or medium mixing bowl, whip the eggs and sugars until they reach the "ribbon stage" or until fluffy. This helps to give the whole wheat brownies that nice crackling top! *If using a stand mixer for this stage, I recommend mixing on speed 6 for about 90 seconds.
- Add in vanilla and melted butter. Mix until combined.
- Now, slowly add in your flour mixture and fold until just combined. Do not overmix!
- Pour into prepared pan and bake for about 30-35 minutes or until the brownies are just set to touch. They will continue to cook as they cool. You don't want it to be jiggly, just set to touch.
- Remove the pan from the over and allow the whole wheat fudgy brownies to cool on a cooling rack before cutting. Cut and serve. Enjoy!