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Do you love a warm, chewy M&M cookie—but also want to incorporate nourishing, fiber-rich foods into your family’s diet?

This Fresh-Milled M&M Cookie strikes that balance beautifully. It’s perfectly sweet, delightfully chewy, and made with wholesome, freshly milled flour.

Baking cookies with fresh-milled flour does take a few thoughtful adjustments to avoid a grainy texture, but I’ll walk you through every step so you can get it right the first time.

Let’s take a classic treat and turn it into a truly nourishing dessert your whole family will love.

Why Fresh-Milled Flour Works in Cookies

Freshly milled flour is the true, unsung hero. This teeny wheat berry is packed full of nutrition, containing about 40 of the 44 essential nutrients needed for humans to thrive.

Below is a chart detailing all of the nutrition available in the humble wheat berry.

✨If you’d like to learn more about what a wheat berry is and all of its nutrients, check out this post!

What Makes These M&M Cookies Special

Freshly milled flour isn’t just nutritious—it greatly enhances flavor. After getting so used to whole wheat flours, our family truly does not enjoy all-purpose baked goods. Even if I decide to bake something with all-purpose flour, I have to add some freshly milled flour to improve the flavor. Milling grains certainly spoils a person.

That being said, it is very important to know what type of wheat berry to use.

Some baked goods do not need strong gluten, like cookies, muffins, pancakes, etc. It is important to know when to use a low-protein wheat. I like to use soft white wheat in my cookies. You can absolutely use other wheats with a low protein content—ancient grains are also a great choice for cookies due to their gentler gluten structure.

✨Check out my post here, if you want to learn more about how to use different wheat berries!

Tools You’ll Need

• Grain mill
• Mixing bowl
• Mixing spoon
• Measuring utensils
• Measuring cups
• Kitchen scale
• Small saucepan
• Cookie scoop (my most favorite tool, ever)
• Baking sheet
• Parchment paper

✨Are you interested in more fresh-milled baking tools that I find helpful? Then check out this post!

Ingredients

• Fresh milled soft white and hard white wheat
• Baking soda
• Salt
• Unsalted butter
• Sugar
• Vanilla extract
• Room temperature eggs
• M&Ms

Step-by-Step: How to Make Freshly Milled M&M Cookies

Step 1: Mill the Grain

Freshly mill your soft white wheat. Set out your eggs.

Step 2: Melt the Butter

Melt your butter in a saucepan over low heat.

Step 3: Slightly Bubble the Sugar

Once the butter is melted, pour in the sugar and stir occasionally as you allow the sugar and butter mixture to bubble—the butter and sugar will not incorporate entirely.

Step 4: Let Cool

Remove the saucepan from the heat and let cool for at least 5 minutes.

Step 5: Combine Wet and Dry Ingredients

Add the baking soda, salt, and vanilla and stir until combined. Add the room temperature eggs and mix thoroughly. Pour the liquid mixture into the flour and stir until no dry flour remains.

Step 6: Mix in the M&Ms

Mix in the M&Ms until they are evenly dispersed.

Step 7: Let Dough Rest in Fridge

This step is absolutely crucial. I recommend an absolute minimum of a 4-hour cold rest in the fridge. Overnight is best. Above are examples of what your dough should look like before and after the fridge rest.

Step 8: Shape

Here you have some flexibility as to the size of your cookie. The cookies you see images for are large cookies. I used a 4 tbsp cookie scoop. But you can absolutely make smaller sizes to suit your needs. A 2 tbsp cookie scoop will get you small cookies, and 3 tbsp a medium sized cookie.

Step 9: Bake

Preheat the oven to 375°F. Line a baking tray with parchment paper.

Recommended bake times by cookie size:

• 2 tbsp: 8–10 minutes
• 3 tbsp: 10–12 minutes
• 4 tbsp: 13–15 minutes

It is imperative that the dough remains cold while you scoop and shape. Work with one tray at a time. As soon as the dough for a tray is scooped, place the dough back into the fridge until you are ready to make the next batch.

To prevent excessive spreading, form the dough into smooth balls and bake immediately.

For chewy cookies, remove them from the oven when the edges are just barely golden. The centers will look underbaked—this is correct.

If you want a pretty M&M topping, gently press additional M&Ms onto the cookies immediately after removing them from the oven. This must be done right away or they will not adhere.

Let cool slightly and enjoy.

Fresh-Milled M&M Cookies

• Prep Time: 20 minutes
• Chill Time: 4 hours minimum
• Bake Time: 9–15 minutes
• Yield: 12–16 cookies (depending on size)

Note: Using a kitchen scale is highly recommended when working with fresh-milled flour. Volume measurements are provided as a convenience.

Ingredients

• 12 tbsp unsalted butter
• 210 g sugar (about 1 cup)
• ½ tsp baking soda
• ½ tsp salt
• 2 tsp vanilla extract
• 2 large eggs, room temperature
• 290 g freshly milled soft white wheat (about 2⅓ cups)
• 170 g M&Ms (about 1 cup), plus more for topping if desired

Step 1 – Prepare Grain

Finely mill the soft white wheat. Set eggs out to come to room temperature.

Step 2 – Melt Butter & Bubble Sugar

Melt the butter in a saucepan over low heat. Add the sugar and stir occasionally, allowing the mixture to gently bubble. Remove from heat and let cool for at least 5 minutes.

Step 3 – Mix Dough

Stir baking soda, salt, and vanilla into the butter mixture. Add eggs and mix thoroughly. Pour mixture into the flour and stir until no dry flour remains. Fold in M&Ms until evenly distributed.

Step 4 – Chill Dough

Cover and refrigerate dough for a minimum of 4 hours. Overnight is best.

Step 5 – Shape & Bake

Preheat oven to 375°F. Line a baking tray with parchment paper. Scoop cold dough into balls (2 tbsp for small, 3 tbsp for medium, 4 tbsp for large cookies). Keep dough cold and work with one tray at a time.

Bake:

• 2 tbsp: 8–10 minutes
• 3 tbsp: 10–12 minutes
• 4 tbsp: 13–15 minutes

Remove when edges are lightly golden and centers look soft. If desired, press extra M&Ms onto cookies immediately after baking. Let cool slightly before serving.

Tips for the Best Results

Here are a few tips that I find helpful when baking cookies with freshly milled flour:

• A very, very finely milled grain is essential to avoid a gritty cookie
• A kitchen scale helps to get consistent results
• Bubbling the butter and sugar helps to evenly coat the milled grains
• An overnight fridge rest with the finished dough gives the best results
• Working quickly and keeping the dough cold while shaping is crucial
• Do not flatten the dough when shaping—bake as a completely round ball

Storage and Freezing

These cookies stay fresh for 3-5 days…though I doubt they will last that long!

I recommend storing in an airtight container. A glass cookie jar is always so pretty to use.

If you choose to freeze cookie dough, simply shape them, lay on a parchment-lined tray and place in the freezer. Once the dough is fully frozen, place in a freezer bag and label. Add 2-3 minutes if you are baking dough from frozen—I find thawing to be unnecessary.

Alternatively—you can freeze baked cookies. Just place completely cooled cookies in a freezer bag, remove excess air, and freeze.

Variations

This recipe is the perfect base for any cookie made with freshly milled flour.

Variations we love include:

• Dark chocolate chips
• White chocolate chips and macadamia nuts
• White chocolate chips and Craisins
• Butterscotch chips

Please note: do not exceed 170 g of add-ins for best results. While slightly more may work depending on the add-ins used, exceeding this amount can affect how the cookies bake.

FAQ

Can I use store-bought whole wheat flour instead of freshly milled?

Yes, you can use whole wheat flour. It will not have the exact nutritional value of freshly milled flour, but it will still be delicious.

What type of wheat berries work best for freshly milled cookies?

Soft white wheat works very well for freshly milled cookies.

Can I make the cookie dough ahead of time or freeze it?

Absolutely! Your dough will perform its best with a long rest in the fridge. I like to make the dough in the evening and rest it in the fridge overnight. The cookies also bake very well from frozen.

Why do fresh-milled cookies have more chew than cookies made with all-purpose flour?

Fresh-milled flour contains the full bran and germ of the wheat, which naturally adds structure and a subtle chew to baked goods. While these cookies are soft and not gritty, a bit of whole-grain texture is normal and part of what makes fresh-milled desserts different from white-flour cookies.

Fresh-Milled M&M Cookies are a really fun treat for your family. I hope this recipe has given you the confidence to bake freshly milled cookies soon and often!

What are your favorite add-ins for freshly milled cookies? I’d love to hear in the comments below!

Blessings,

Payton