Fresh Milled Brown Butter Chocolate Chip Cookies
Fresh milled flour recipes are the new sourdough, and this amazing fresh milled brown butter chocolate chip cookie recipe is one you won’t want to sit on.
Chewy and full of chocolatey goodness, the warm flavor of brown butter pairs perfectly with the nuttiness of freshly milled flour for a delicious chocolate chip cookie packed with deep flavor.

Using fresh milled flour makes this brown butter chocolate chip cookie a nutrient dense treat, as the freshly milled flour contains vitamin E, magnesium, manganese, iron, folate, zinc, vitamin B6, antioxidants, and enzymes.
Talk about packing a punch! Pair these chewy cookies with a glass of raw milk for a nutrient dense, cozy afternoon treat.

And if you feel like getting a little fancy, top these delicious fresh milled brown butter chocolate chip cookies with sea salt for the perfect finishing touch!

Chewy Brown Butter Chocolate Chip Cookies (with Freshly Milled Flour)
Equipment
- Electric hand mixer
Ingredients
- 1½ cup + 1 Tbs freshly milled flour I use hard white wheat
- ½ tsp salt
- ¼ tsp baking soda
- 5 Tbs unsalted butter divided
- ¼ cup sugar
- ½ cup brown sugar
- 1 tsp vanilla extract
- 1 large egg room temperature
- ½ cup chocolate chips plus extra for topping the cookies
- 1 Tbs coarse sea salt for sprinkling
Instructions
- Combine the freshly milled flour, salt, and baking soda in the small mixing bowl and whisk until combined. Set aside.
- Brown three tablespoons of the butter in a small saucepan, and then add to the remaining two tablespoons of butter in the medium mixing bowl. Add the sugars and cream with the hand mixer on medium spead for about 30 seconds.
- Add the egg and vanilla and mix on medium speed for about 30-60 seconds.
- Add the dry ingredients to the wet ingredients and mix until just combined. Add the chocolate chips and mix until distributed. Place uncovered in the freezer and chill for 30 minutes.
- Meanwhile, preheat the oven to 375 degrees Fahrenheit and line a baking sheet with parchment paper.
- Scoop and roll the chilled cookie dough in to balls, about 2 Tablespoons of dough each, and arrange 3-2 inches apart on the prepared baking sheet.
- Bake for 9-11 minutes, and remove the cookies when the edges are set but the center still appears slightly soft.
- Press a few additional chocolate chips into each cookie and sprinkle with course sea salt. Allow the cookies to cool on the sheet for 5 minutes, and then remove to the cooling rack for 10 more minutes.
Notes
Kitchen Equipment
- Electric hand mixer
- Medium sized mixing bowl
- Small mixing bowl
- Baking sheet
- Parchment paper
- Cooling rack
Ingredients to Note (for Fresh Milled Brown Butter Chocolate Chip Cookies)

Brown sugar – Using more brown sugar than white sugar in this recipe helps get that amazing chewy texture.
Fresh milled flour – I used a hard white wheat berry for this recipe, but you can use whatever is your preferred variety of wheat berry.
Brown butter (unsalted) – Browning the butter gives chocolate chip cookies a delicious, nutty flavor; but browning all of the butter in this recipe makes the cookies spread too much. That’s why this recipe calls for browning 3 tablespoons, and leaving the rest unbrowned. (See below for instructions on browning butter.)
Using unsalted butter allow you to better control the overall salt content of the fresh milled brown butter chocolate chip cookie, as different varieties of butter will vary in their salt content.
Chocolate chips – I like using semi-sweet or dark chocolate chips or chunks; but use whatever you prefer.
Course sea salt – Topping these chewy brown butter chocolate chip cookies with course sea salt gives the perfect salty contrast and crunch the cookies need.

Tips for Fresh Milled Brown Butter Chocolate Chip Cookies
Spoon and level the flour – Spooning and leveling the flour allows you to better control how much flour you use and avoids packing the flour in. (See below for more info on how to spoon and level flour.)
Brown part of the butter – Browning only part of the butter gives these cookies that delicious brown butter flavor but keeps them from spreading too much.
Use a room temperature egg – Using a room temperature egg allow the ingredients to mix better.
Chill the dough – Chilling the dough in the freezer, uncovered, keeps the cookies from spreading too much and yields a delicious chewy interior. Be careful not to leave it chilling for past 30-40 minutes, as this will result in cookies that don’t spread enough.
Storage Instructions
To store these cookies, keep them in an airtight container at room temperature for up to 4 days, or in the refrigerator for up to one week.
What is brown butter?
Brown butter is simply regular butter that has been browned until it reaches a particular color. It gives off a warmer, nuttier flavor and is the perfect addition to these freshly milled brown butter chocolate chip cookies.
How to make brown butter
You can make brown butter by simply warming the salted butter in a small saucepan over medium heat. Once it is fully melted, watch for it to begin to turn brown.
When it is a medium brown color, is beginning to foam, and is yielding a nutty aroma, remove the browned butter from the heat.

How to Spoon and Level Flour
Spooning and leveling flour keeps the flour measurement more exact and prevents packing of the flour.
To spoon and level the flour, simply scoop the freshly milled flour with a spoon into your measuring cup, and then, without shaking the flour down, use the flat side of a butter knife to level the extra flour off the top of the measuring cup. Repeat for each measuring cup of flour.
Why use freshly milled flour?
Freshly milled flour is such an amazing superfood (containing vitamin E, magnesium, manganese, iron, folate, zinc, vitamin B6, antioxidants, and enzymes, just to name some).
Our of the 44 essential nutrients the human body needs, freshly milled flour contains 40 of them! Who knew a freshly milled brown butter chocolate chip cookies could contain so much nutrition?
Many of the nutrients in the freshly milled flour, however, will begin to deteriorate when exposed to oxygen (which occurs when the wheat berries are milled).
Most sources agree that consuming the flour within 72 hours of milling is the best way to utilize all the amazing benefits of freshly milled flour before their deteriorate.
For more info on the amazing benefits of freshly milled flour, check out this article.
What kind of wheat berry should I use?
While there are some general uses for different wheat berries, it really boils to personal preference. In this recipe I used hard white wheat berries (Prairie Gold to be specific). Below are a few general guidelines if you are new to the terms.
Hard red wheat – These wheat berries produce a flour high in protein, and therefore are great for bread recipes as they develop a nice amount of gluten. They will yield a hearty whole wheat bread!
Hard white wheat – Hard white wheat berries still have a decent amount of protein, but have a milder flavor, making them ideal for bread, but also other baked goods such as tortillas, and cookies.
Soft white wheat – Thes wheat berries have a lower protein and gluten content and yield a more delicate crumb, making them ideal for pastries and cakes.
There are so many other varieties, including ancient grains such as Kamut or Einkorn. For additional information, check out this article.
Instructions for Fresh Milled Brown Butter Chocolate Chip Cookies
- Combine the freshly milled flour, salt, and baking soda in the small mixing bowl and whisk until combined. Set aside.

2. Brown three tablespoons of the butter in a small saucepan, and then add to the remaining two tablespoons of butter in the medium mixing bowl. Add the sugars and cream with the hand mixer on medium speed for about 30 seconds.

3. Add the egg and vanilla and mix on medium speed for about 30-60 seconds.
4. Add the dry ingredients to the wet ingredients and mix until just combined. Add the chocolate chips and mix until distributed. Place uncovered in the freezer and chill for 30 minutes.

5. Meanwhile, preheat the oven to 375 degrees Fahrenheit and line a baking sheet with parchment paper.
6. Scoop and roll the chilled cookie dough in to balls, about 2 Tablespoons of dough each, and arrange 3-2 inches apart on the prepared baking sheet.

7. Bake for 9-11 minutes, and remove the cookies when the edges are set but the center still appears slightly soft.
8. Press a few additional chocolate chips into each cookie and sprinkle with course sea salt. Allow the cookies to cool on the sheet for 5 minutes, and then remove to the cooling rack for 10 more minutes.

More Cookie Recipes
For more cookie recipes, check out my thick and chewy pumpkin sourdough snickerdoodle recipe.