These delicious whole wheat brownies with freshly milled flour are remarkably tender, chocolatey, and rich – the sweet treat we all love, but now with a nourishing whole grain bonus.

These whole wheat brownies don’t shout healthy. They don’t shout whole wheat, either, unless you’re referring to the nutty flavor and pleasant, wholesome texture. You’ll find that the fresh milled flour enhances the brownies rather than feeling like a healthy compromise.
The best brownies are tender, rich, and a bit crackly on top, and these whole grain brownies are all of those things. They’re simple enough for a casual weeknight dessert, but have the flavor and impression of effort that would be wonderful for special occasions, as well.
With melted chocolate chips, real butter, and warm vanilla extract, these decadent brownies are sure to satisfy your sweet tooth and please the whole family.
You can enjoy a batch of these brownies in under an hour, which is helpful if you didn’t plan on dessert but need some quick ideas. Other quick dessert options are sourdough discard monster cookies, homemade apple pie, or a tangy-sweet berry crisp.
Fresh ground wheat flour elevates recipes with flavor and nutrition that processed flours simply cannot match. But milling your own grains often involves a learning curve, sometimes resulting in dense, crumbly, or even coarse bakes. Don’t be discouraged! Try these easy to follow recipes for a fresh milled Dutch baby pancake, whole wheat biscuits, fresh milled chocolate chip cookies, or fresh milled sourdough dinner rolls.
If you’re new to fresh ground wheat, I have a post called How to Mill Your Own Flour at Home that should be very helpful! If you’d like to learn more about sourdough, start with How to Use Sourdough Starter and Maintaining and Feeding a Sourdough Starter.
Why You’ll Love This Recipe
Delicious flavor – Fresh milled grains add a depth and complexity of flavor that is earthy and robust. Combined with melted chocolate, vanilla, and cocoa powder, this brownie recipe is absolutely delightful.
Tender crumb – These brownies bake up tender and moist. Underbake them a touch for more fudgy brownies, or bake them a touch longer for a more cake-like brownie.
Wholesome ingredients – Made with full-fat butter, farm fresh eggs, homemade vanilla extract, quality chocolate chips, and whole grain flour milled right at home, this sweet treat is deliciously wholesome.
Ingredients

Sugar – This recipe calls for regular white sugar, but you can substitute brown sugar if you’d like.
Chocolate chips – Use quality chocolate chips for the best flavor.
Flour – I use soft white wheat berries for this recipe. 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.
Eggs – Use two whole eggs and one egg yolk. Save that egg white to add to your high-protein scrambled eggs or as an egg wash for homemade sourdough Italian bread.
A full ingredient list with exact amounts can be found in the recipe card below.
Tools You May Need
Mockmill – This is the grain mill that I use. Read my review on the Mockmill versus Nutrimill for more information on why I chose this specific mill.
How to Make Fresh Milled Flour Brownies

Step 1: Preheat your oven to 350 degrees Fahrenheit. Prepare an 8×8 pan with parchment paper or brush it with butter.

Step 2: In a medium saucepan, add sugar, chocolate chips, and butter. Melt over low heat, whisking until smooth and shiny. Set aside to cool for a few minutes.

Step 3: In a separate bowl, mix flour, salt, and cocoa powder.

Step 4: In the bowl of a stand mixer – or in a mixing bowl with an electric mixer – add eggs, egg yolk, and vanilla. Mix until frothy. Reduce the speed to low and slowly add the chocolate butter mixture to the eggs. Pour a little bit at a time so the eggs don’t curdle. Continue mixing until well combined.

Step 5: Fold in the dry ingredients and mix-ins, if desired.

Step 6: Pour batter into the prepared pan and spread evenly. Bake for 25-35 minutes or until the center has set. Baking time may vary, but look for a shiny top crust and no wobbling in the center. Let them cool to firm up and make slicing easier.

Tips
- For best results, mill your flour right before making the recipe.
- Some mix-in suggestions are additional chocolate chips, chopped nuts, or dried fruit. You could also drizzle warmed peanut butter over the top and swirl it into the brownies with a knife before baking.
- Let the batter rest for 10 minutes before baking to soften the whole grains and improve the texture.
- These homemade brownies will firm up as they cool. Underbake slightly for fudgy brownies, or bake the full time (or a touch more) for more cakey brownies
- Cool completely to make slicing clean and easy.
Recipe FAQs
Store leftovers in an airtight container at room temperature for 3-4 days, or refrigerated for 5-7 days. These brownies also freeze well when wrapped up securely. Thaw at room temperature.
Sure! You can double for two 8×8 pans, or use a 9×13 and increase the bake time until the center is set.
Yes, fresh milled flour retains all parts of the grain, making it more nutritious, filling, and overall wholesome than other processed flours. It’s also fresh, so it retains more of its nutrients than flour that has been milled and exposed to air and light over time.
Soft white wheat berries are best for more delicate recipes like cookies, cakes, and pastries. If you only have hard white wheat, you can still use it in this recipe, but the texture may be heavier and denser.
While these do contain refined sugar, this recipe pulls together many wholesome, real food ingredients to create an amazing brownie. It’s high-calorie, but simple, made with nourishing and fresh ground whole wheat (which is more nutritious than all purpose flour), and contains no fillers or artificial ingredients. It’s a dessert you can feel good about!
More Cookie Recipes from the Farmhouse
If you try this recipe and love it, I would love it if you could come back and give it 5 stars! Tag me on Instagram @farmhouseonboone.
Whole Wheat Brownies with Freshly Milled Flour

Equipment
Ingredients
- ¾ cup sugar, 175 grams
- 1 cup chocolate chips, 172 grams
- ½ cup butter, 114 grams
- ⅔ cup soft white wheat flour*, 94 grams
- ¼ teaspoon salt
- ⅓ cup cocoa powder, 40 grams
- 2 eggs, plus 1 egg yolk
- 2 teaspoons vanilla extract, 10 grams
- ½ cup mix-ins, optional
Instructions
- Preheat your oven to 350 degrees Fahrenheit. Prepare an 8×8 pan with parchment paper or brush it with butter.
- Add sugar, chocolate chips, and butter to a saucepan and melt over low heat. Whisk until the sugar dissolves and the mixture is smooth and shiny. Set aside to cool.
- In a separate bowl, mix flour, salt, and cocoa powder.
- In the bowl of a stand mixer, add eggs, egg yolk, and vanilla. Mix until frothy. Turn the stand mixer on low and slowly add the chocolate butter mixture to the eggs. Pour a little bit at a time so the eggs don’t curdle. Continue mixing until well combined.
- Fold in dry ingredients and mix-ins, if desired.
- Transfer to the prepared baking dish and spread evenly. Bake for 25-35 minutes or until the center has set.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.


















