Best Freshly Milled Chocolate Chip Cookies (or store flour)

January 8, 2026
by: Winnie
6 Comments
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Updated: January 9, 2026

“It’s got the crunch and the chew! The best chocolate chip cookie of my life.” That is not my quote. That is my husband’s very serious, no-nonsense review of these freshly milled chocolate chip cookies. And honestly? I trust his cookie judgment with my life.

I am always on a quest for the ultimate recipe. Always. Because if I’m going to waste calories on sugar, then I want it to be worth it. Consequently, I have made hundreds … yes, hundreds … of freshly milled chocolate chip cookies over the years (which can also be made with store-bought flour). Eventually … after many batches, many crumbs, and many “almost but not quite” moments … I found the one. You know the feeling when something is just right? That was this. The hunt was officially over. Forever.

So, allow me to formally introduce you to your new favorite fresh milled chocolate chip cookies (or you can make them with store-bought flour, too).

Brown the Butter (yes, we’re starting with the hard part) for Freshly Milled Chocolate Chip Cookies

If I could change one thing about this recipe, it would be this: I wouldn’t put the hardest step first. Ideally, I’d let you eat a cookie before asking you to brown butter so you’d understand why this is non-negotiable.

Because, unfortunately, you can’t skip this step. And there are two very good reasons why.

First, browned butter adds a deep, caramel-like flavor that makes freshly ground chocolate chip cookies taste beyond bakery-level fancy. Honestly, who doesn’t want caramel notes in their cookie?

Second, we need to remove some water from the butter. Since we’re using sourdough discard (which adds flavor but also moisture), this step creates balance. And balance, in cookies and in life, is everything.

Now, the good news? Browning butter is easy. The bad news? It adds a few extra minutes to your bake. Still worth it.

How to Brown Butter (without crying) for Freshly Milled Chocolate Chip Cookies

First, grab a medium-sized pot (I use a 2 quart). You might be thinking, “We’re only melting two sticks of butter … why not a small pot?” And while you’re not wrong … browned butter gets foamy and ambitious. Therefore, we need space so it doesn’t crawl out of the pan like it’s escaping.

Next, add two sticks of butter to the pot and place it over medium heat. As it melts, it will bubble, sizzle, and cook off the water. Eventually, the milk fats will sink to the bottom and start browning. At that moment, reduce the heat to low and stir constantly. Do not answer your phone. Do not walk away. Because while the butter is seconds away from caramel perfection, it is also seconds away from burned sadness.

Once it smells nutty and looks golden with brown bits at the bottom, remove it from the heat immediately.

Toasty Nuts (trust me on this) for Freshly Milled Chocolate Chip Cookies

You might be thinking, “I don’t like nuts in cookies.” To that I say: same.

In fact, when I first started making these homemade chocolate chip cookies with freshly milled flour, I didn’t include nuts at all. That changed after my daughter and her husband went to New York City and brought me home a chocolate chip cookie from Levain Bakery. That cookie had walnuts in it. And shockingly, for the first time in my life, the nuts made the cookie better.

Because this is a hearty cookie, the structure pairs beautifully with nuts. So, naturally, I tried adding walnuts to my next batch. And just like that, the cookie entered perfection territory.

How to Toast Nuts for Freshly Milled Chocolate Chip Cookies

While your butter is doing its caramel thing, let’s multitask.

Add ½ cup of walnuts or pecans to a dry skillet … no oil, no butter. Place it over medium heat and stir or shake the pan frequently so nothing burns. After 3–5 minutes, when they smell amazing and look lightly browned, remove the nuts from the heat and let them cool.

They’ll be cooled enough when the dough is ready for them.

Butter & Sugar (where magic begins) for Freshly Milled Chocolate Chip Cookies

In a large mixing bowl, add your browned butter. It’s okay if it’s still warm, or if it’s cooled a bit. Just make sure you scrape every single brown bit out of the pan … those bits are pure flavor gold.

Next, add both the white sugar and brown sugar. Mix until fully combined, and then keep mixing for a few minutes.

Egg Yolks for Freshly Milled Chocolate Chip Cookies

Now it’s time to add the three egg yolks. And yes, only the yolks.

Why? Because egg whites are mostly water. Since we’re already adding sourdough discard … extra liquid would throw off the texture. Using only yolks keeps these freshly milled chocolate chip cookies rich, chewy, and perfect.

If you hate wasting food (same), I’ve got you covered. I have an excellent recipe for chocolate meringue cookies that uses exactly three egg whites. You can refrigerate the whites for up to four days or freeze them for later (a bake now or bake later scenario). Click here for that free recipe.

Add the egg yolks to the bowl and mix for 2–3 minutes. If the mixture looks greasy or separated, don’t panic. It will come together after we add a few more things.

Sourdough (flavor level: elevated) for Freshly Milled Chocolate Chip Cookies

Next, add 1 cup of sourdough discard (or starter) and 1 teaspoon of vanilla extract. This is one of my favorite ways to use sourdough discard … because it adds a subtle tang that makes these sourdough chocolate chip cookies stand out.

Stir well. At this point, the batter will start looking smooth and cohesive.

Dry Stuff for Freshly Milled Chocolate Chip Cookies

Now add the following directly to the mixing bowl:

1 teaspoon of baking powder
1 teaspoon of baking soda
1 teaspoon of salt

Give them a good swirl with everything else in the mixing bowl.

The baking powder gives the cookies a lift … making for a cakier and fluffier texture. Meanwhile, the baking soda makes them spread a bit and chewier (by reacting with the molasses in the brown sugar). Together, they strike the perfect balance. I think this is the secret to why my husband can say, “These cookies got the crunch and the chew.” And honestly, that’s the goal!

Freshly Milled Flour

Now for the reason we’re all here: freshly milled flour.

(So no one feels left out, I have also included a recipe card using store-bought flour at the bottom. And if you’re wondering why anyone would go through the extra step of milling their own flour, I’ve got you covered there too … with a post that breaks down the health benefits and another that gives a simple, no-overwhelming overview of freshly milled flour.)

But if you’re already a freshly milled flour nerd like I am, let’s talk wheat berries.

Choosing Wheat Berries for Freshly Milled Chocolate Chip Cookies

Soft wheat berries: Excellent choice. Low gluten means fluffier cookies.
Ancient grains (einkorn, emmer, spelt, Khorasan/kamut): Also great. Nutritious and tender.
Mixing grains (soft and ancient): Absolutely encouraged.
Hard wheat berries: Not recommended. High protein = Too much gluten development = Tough cookies.

Measure out 420 grams (or 2¼ cups) of wheat berries, grind them finely, then add the flour to the bowl. Mix on low speed just until combined.

Now, here’s a little wheat berry wisdom: “Yeast/sourdough likes it hard. Baking soda/powder likes it soft.” Translation? Bread wants the strength of hard wheat, but cookies prefer the gentle touch of soft wheat. If you’re curious about becoming a grain matchmaker, here’s a whole article waiting to guide you through the wheat berry choosing process.

Insert Yummies into the Freshly Milled Chocolate Chip Cookies

Now comes the fun part!

Gently fold in:

Chocolate Chips: You can use 2½ cups of semi-sweet chocolate chips. However, for maximum flavor and texture, I recommend a mix of sizes (mini to chunky) and cocoa levels (milk to dark). My favorite mix is:
- 100 grams: mini size + semi-sweet (like Nestle mini)
- 150 grams: varied sizes + milk chocolate (milk chocolate candy bar chopped up)
- 100 grams: chunks + dark chocolate (like Ghirardelli 60%)
- 150 grams: regular size + semi-sweet (like Nestle regular)
Nuts: Remember those nuts that you gently toasted at the beginning. Well, now is the time to add them. They have cooled off just enough to be ready to shine.
Whole Flax Seeds: Yes, it’s a little weird. And yes, it works. They add fiber, nutrition, and the occasional surprise crunch. These cookies are almost granola-adjacent … hearty enough to actually feel satisfied after one (or twelve … no judgment).

Mix in all these yummies either with your mixer or with a spatula. The goal is to evenly distribute the goodies.

Scoop the Freshly Milled Chocolate Chip Cookies

Once your dough is fully mixed and loaded with all the good stuff, it’s time to slow things down a bit. First, line a baking sheet with parchment paper. Then, using a medium #40 (2-tablespoon) cookie scoop, portion the dough into neat little mounds. This scoop size is my personal favorite for freshly milled chocolate chip cookies because it creates a cookie that’s thick, hearty, and perfectly balanced … crisp on the edges, chewy in the middle, and sturdy enough to hold all that chocolate.

Of course, if you prefer a bakery-style giant cookie or a smaller, snackable version … feel free to adjust the size. Just keep in mind that changing the size will also change the baking time. That said, uniform dough balls … thanks to a scoop … mean evenly baked cookies and far less second-guessing. No more wondering if that last cookie is mysteriously larger than the first one.

Chill (the waiting game) Freshly Milled Chocolate Chip Cookies

Once the tray is full, cover it tightly with plastic wrap. Now comes the hardest part: put it in the refrigerator and walk away. The dough needs to chill for at least 3 hours, but honestly, overnight is where the magic happens. You can even let these fresh milled chocolate chip cookies rest for up to 48 hours if you want a deeper flavor and a more developed texture.

So what’s actually happening while the dough is hanging out in the fridge?

Freshly milled flour fully hydrates, which softens the bran and improves the overall texture.
Browned butter firms back up, preventing the cookies from spreading into thin, sad puddles.
Flavors have time to mingle, deepen, and become very good friends.
The structure of the dough improves, giving you thicker cookies with better lift.
Sourdough slowly does its thing, adding a subtle tang that makes these freshly ground flour chocolate chip cookies extra special.

In short, chilling isn’t just a suggestion … it’s the secret to those crisp edges and chewy centers everyone fights over.

Personally, I always make the dough one day and bake the cookies the next. Not only does it make baking day feel easier, but it also guarantees that every batch of freshly milled chocolate chip cookies comes out exactly how I want them: bold in flavor, beautifully textured, and absolutely worth the wait.

Bake & Cool (the moment we’ve been waiting for) the Freshly Milled Chocolate Chip Cookies

After all that patience and chilling … it’s finally go time.

First, preheat your oven to 350°F. This temperature is the sweet spot for sourdough chocolate chip cookies because it allows the cookies to bake evenly … giving the centers time to puff while the edges turn golden and crisp without overbrowning.
Next, line two baking sheets with parchment paper. Parchment not only prevents sticking, but it also helps regulate heat so the bottoms of your cookies don’t brown too quickly. In other words, parchment is doing quiet, behind-the-scenes work that makes your cookies better.
Now, place 8 dough balls per baking sheet, spacing them out generously. Even though the dough is chilled and well-structured, these freshly milled chocolate chip cookies still need room to spread and breathe. Crowding the pan leads to cookies that bake into each other, and while that sounds cozy, it’s not ideal.
Before the cookies go into the oven, sprinkle each one with a pinch of flaky sea salt. This step may seem optional, but I don’t think so. The salt enhances the sweetness, sharpens the chocolate flavor, and adds that irresistible sweet-and-salty contrast that makes people reach for “just one more.”

Slide the baking sheets into the oven and bake for 12–14 minutes. Keep an eye on the edges rather than the centers. When the edges are lightly golden and set, the cookies are done … even if the centers still look soft and puffy. That softness is exactly what you want.

Once the cookies come out of the oven, resist the temptation to move them immediately. Let them rest on the baking sheet for 10 minutes. During this time, the freshly milled chocolate chip cookies finish setting up, firming just enough to hold together, which prevents them from falling apart when you move them.

After that, carefully transfer them to a wire rack. This allows air to circulate underneath, preventing soggy bottoms and stopping the residual heat from overcooking the cookies.

And finally … this is important … pour yourself a glass of cold milk, grab a warm, freshly milled chocolate chip cookie, and take a moment. Because after all that browning, chilling, and waiting … life really is very good.

FAQ about Freshly Milled Chocolate Chip Cookies

How do you store freshly milled chocolate chip cookies?

Store in an airtight container for up to 5 days … or until they mysteriously disappear.

Can you freeze freshly milled chocolate chip cookies?

Yes, you have two excellent options.

Freezing the Dough Balls: After scooping the dough, place the freshly milled chocolate chip cookie dough balls on a baking sheet and freeze them until solid. Once frozen, transfer them to a freezer-safe bag or airtight container. This method is perfect because you can bake exactly the number of cookies you want, whenever you want them. There’s no need to thaw … just bake straight from frozen and add 1–2 extra minutes to the baking time. This is especially dangerous (in the best way possible) if you love ending the day with a warm cookie after dinner.
Freezing Baked Cookies: You can also bake all the freshly milled chocolate chip cookies at once and freeze them after they’ve completely cooled. Store them in an airtight container or freezer bag, ideally with parchment between layers to prevent sticking. When the craving hits, you can let them thaw at room temperature or enjoy them straight from the freezer. Surprisingly, frozen freshly milled chocolate chip cookies are excellent.

Can I double this recipe?

Absolutely. You should.

Which chocolate should I use?

I follow one very simple rule: if you wouldn’t happily eat it straight out of the bag, it doesn’t belong in the cookie. The chocolate is a major player here, not just a background character, so quality matters.

Why the nuts inside the cookie?

They add texture, giving the cookie something to bite into. They add flavor, especially when lightly toasted. And they add contrast, breaking up the richness of the chocolate and dough. There’s also a bit of tradition here … nuts were part of the original Toll House chocolate chip cookie recipe, so in a way, this is a nod to cookie history. Once you try them, it’s hard to go back.

Why the sprinkle of salt on top?

Salt enhances sweetness rather than competing with it, which means the cookie tastes richer and more balanced instead of overly sugary. Additionally, the contrast of salty flakes against melty chocolate creates that sweet-and-salty moment that makes people pause mid-bite and say, “Wow.”

Why are my cookies flat?

If your freshly milled chocolate chip cookies (or cookies made with store-bought flour) spread too much, don’t panic … there are usually two simple reasons. First, the butter may have been too warm or not fully re-solidified. That’s why chilling the dough is so important. Warm butter melts too fast in the oven, causing the cookies to spread. Second, there may not be enough flour. Accurate measuring really matters. Too little flour means less structure, which leads to flat cookies.

Conclusion: Why Freshly Milled Chocolate Chip Cookies Are Worth Every Single Step

The chocolate chip cookie is widely considered Pennsylvania’s state cookie, and since I’m from Pittsburgh … my affection for it runs deep and personal. However, even beyond state pride, the chocolate chip cookie holds a special place in just about everyone’s heart. Americans consume billions of chocolate chip cookies every single year, which begs an important question: if we’re going to eat that many, why not make the very best version?

These freshly milled chocolate chip cookies aren’t just another cookie recipe. They’re the result of years of testing, tweaking, baking, and re-baking in search of that perfect balance. They’re rich without being heavy, chewy without being dense, and crisp on the edges while staying soft and satisfying in the center. Every ingredient has a purpose, every step adds value, and every bite proves that the extra effort is worth it. They’re also the kind of cookie that creates moments. The kind you bake for family gatherings, tuck into lunchboxes, or sneak off the cooling rack when no one’s looking.

Don’t forget to grab the free recipe card for chocolate meringue cookies … because those three leftover egg whites deserve a happy ending. Trust me, you won’t be even a little sad about it. These cookies are absolutely amazing, too.

Don’t want to miss a recipe like this? Subscribe here and join the inner circle. As a thank-you, I’ll send you a printable recipe card for the best pancakes on earth (my Mom’s secret recipe).

If you bake these freshly milled chocolate chip cookies, I would absolutely love to hear about it. Leave a comment below, tag me on Instagram (@hopethiswerksdiy) or find me on Facebook … so I can cheer you on from afar … most likely while “quality-testing” another cookie myself.

So until next time, may your chocolate chip cookies always be chewy in the middle, crispy on the edges, and deeply flavorful. Cheers!

Yield: 2 dozen

Chocolate Chip Cookies (freshly milled flour + sourdough)

A next-level sourdough discard chocolate chip cookie with fresh milled flour. Wholesome ingredients, outrageous flavor ... bakery cookies don’t stand a chance. It's got the crunch and the chew.

Ingredients

1 cup (2 sticks) butter
½ cup (100g) walnuts or pecans, toasted and chopped (optional)
1 cup + 2 tbsp (225g) white sugar
1 cup (215g) brown sugar
3 large egg yolks
1 cup (240g) sourdough discard
1 tsp vanilla extract
1 tsp baking powder
1 tsp baking soda
1 tsp salt
2¼ cups (420g) soft white wheat berries, finely ground (substitute: ancient grains)
2½ cups (500g) chocolate chips (I use: milk + dark, big + small ... for maximum chocolate happiness)
1½ tbsp (16g) whole flax seeds (optional)
flaky sea salt, to sprinkle on top of each cookie (sweet needs a little salty friend)

Instructions

Brown the Butter: Do not skip this step ... it's where the flavor lives, and it keeps the moisture from going rogue. Place the butter in a saucepan over medium heat. Cook until melted and foamy, then reduce the heat to low. Watch closely as it turns golden brown and smells nutty (this happens quickly ... one second it's caramely goodness and the next it's burned sadness). Remove from heat. You'll have about 185g of browned butter. Set aside to cool slightly. (1 cup butter)
Toasty Nuts: While your butter is browning, add walnuts or pecans to a dry (no oil) small skillet over low-medium heat. Stir occasionally until fragrant and lightly golden (about 4 minutes). Remove from heat and set aside. I'm not a huge nut fan either, but they do make these cookies next level. (½ cup walnuts or pecans)
Sugar: In a large mixing bowl, whisk browned butter, white sugar, and brown sugar until well combined ... about 2–3 minutes. (1 cup + 2 tbsp white sugar, 1 cup brown sugar)
Add Yolks: Add the egg yolks and whisk on high for 2–3 minutes. It may look greasy or separated right now ... totally normal. Don’t panic. (3 egg yolks)
Sourdough & Vanilla: Mix in sourdough discard and vanilla until smooth and fully combined, about 2–3 minutes. It will now look like thick cake batter. (1 cup sourdough discard, 1 tsp vanilla extract)
Dry Stuff: Mix in baking powder, baking soda, and salt until combined. (1 tsp baking powder, 1 tsp baking soda, 1 tsp salt)
Freshly Milled Flour: Grind wheat berries into a fine flour. Add to the bowl and mix on low speed until just combined. (2¼ cups soft white or ancient wheat berries, ground)
Yummies: Gently fold in chocolate chips, toasted nuts, and flax seeds ... mix just enough to evenly disperse the goodness. (2½ cups chocolate chips, 1½ tbsp whole flax seeds, ½ cup toasted nuts)
Scoop & Chill: Line a baking sheet with parchment paper. Use a cookie scoop (I love a medium #40/2-tablespoon scoop) to scoop the dough ... or not. Nestle the dough balls close together so they all fit on one tray. Cover with cling wrap and refrigerate for 3–48 hours.
Bake & Cool: Preheat the oven to 350°F. Line two baking sheets with parchment paper. Place 8 cookies per sheet and sprinkle with flaky sea salt. Bake for 12–14 minutes, until edges are lightly golden. The centers may look puffy ... perfectly fine. Let cookies cool on the baking sheet for 10 minutes, then transfer to a wire rack to cool completely.
Eat: Grab a cookie. Pour a glass of milk. Life is good!

Notes

Store?

You can store your fresh milled flour chocolate chip cookies in an air-tight container on the counter for up to 5 days ... assuming they last that long.

Freeze?

Dough: Freeze cookie dough balls and bake straight from frozen. Just add 1–2 extra minutes of bake time. Fresh cookies on demand = life upgrade.
Baked: Baked cookies also freeze beautifully and will keep for a few months ... perfect for emergencies, guests, or late-night cravings.

Double the Recipe?

Absolutely. Go for it ... you can never have too many homemade chocolate chip cookies made with fresh ground flour!

Don't want to waste the egg whites?

Grab a FREE chocolate meringue cookie recipe that uses exactly 3 egg whites and turns them into something light, chocolatey, and completely worth it. Click here and give those egg whites a delicious purpose.

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Yield: 2 dozen