Whole Wheat Chocolate Chip Cookie Bars

These whole wheat cookie bars are made with freshly milled flour and they are equally easy and nutritious.

I could extol the praises of freshly milled whole wheat flour all day long. But if you’ve landed on this post, you probably already know all about it.

When you’re working with whole wheat, it can be somewhat tricky to replicate those family-favorite recipes you used to make with all-purpose white flour.

Chocolate chip cookie bars are one of my family’s go-to desserts. They’re easier to make than cookies, honestly.

After some trial and error, I landed on this recipe that turns out excellent whole wheat cookie bars that are just the right balance of chewy and crispy.

Vertical graphic with cookie bars on a plate and cookie bars cooling in a baking pan, with text "whole wheat cookie bars- with fresh milled wheat"

Whole wheat blondies

Some call chocolate chip cookie bars “blondies”, and this recipe might also be called whole wheat blondies.

They’re called blondies because they have a similar texture to a brownie- but with the appearance and taste of a chocolate chip cookie.

Basically, you get the chewy goodness of a cookie, but in an easy to make bar form!

Of course, these cookie bars will naturally be a little darker than typical blondies made with all-purpose flour. But in my opinion, the texture and taste is much better.

By using dark chocolate chips, you also get the benefit of antioxidants, and they typically have a lower sugar content than other types of chocolate chips.

(Try the new dark chocolate chips from Azure Standard, if you haven’t already!)

Tips for better whole grain desserts

When you mill your own whole grains, as your know, you get to keep the bran and germ- and the fiber, B vitamins, and more antioxidants that come with them.

None of that goodness gets sifted out, unless you’re doing the sifting yourself. (In which case, these tips won’t matter to you as much.)

Did I mention that including every part of these whole grains also does wonders for gut health?

Freshly baked whole wheat chocolate chip cookie bars in 9x11 pan

But the drawback, of course (especially if you’re new to whole grains), is that it creates a different texture than some are used to when baking with freshly milled flour.

So what makes a good whole grain dessert? There are a few things that will help your healthy cookie bars taste more like their familiar white-flour counterparts.

Read next: Fresh Milled Flour Fluffy Waffle Recipe

Adjust your mill setting to fine

While milling your soft wheat, you want to make sure adjust your mill to the finest setting. Finer flour results in lighter baked goods.

On my Nutrimill Harvest, I turn on the mill, add the wheat berries, then tighten the knob as far as I can to the right. As long as the flour is coming out in a steady stream, I know it’s not over-tightened.

Let the grains soak

Another easy thing you can do is, after mixing your ingredients per the recipe below, simply let the mixture sit in the mixing bowl for about 15-20 minutes- before adding the chocolate chips and nuts.

Then add your mix-ins (chocolate chips and nuts-optional), and transfer to the baking pan.

This gives your freshly-milled grains some extra time to soak up the liquids, making a softer product in the end.

Cookie bars on a plate , fresh from the oven. With wheat berries and chocolate chips in background.

When making bread with freshly milled flour, I let about half of the flour soak in the water for a few hours. It really makes a difference.

If you try these whole wheat chocolate chip cookie bars, be sure to let us know how you like them!

freshly milled wheat dessert: whole wheat chocolate chip cookie bars

Whole Wheat Chocolate Chip Cookie Bars

Prep Time: 20 minutes
Cook Time: 20 minutes
Additional Time: 20 minutes
Total Time: 1 hour

Healthy cookie bars made with freshly milled wheat. Soft and gooey- a perfect after dinner treat.


  • 3 cups freshly milled soft white wheat flour
  • 2 teaspoons baking soda
  • 3/4 cups salted butter (1.5 sticks), melted
  • 1.5 cups brown sugar (I like to use 1/2 light brown, 1/2 dark brown)
  • 2 eggs
  • 1 teaspoon vanilla
  • 1.5 cups dark chocolate chips
  • 1/4 cup chopped walnuts or pecans (optional)


  1. Preheat oven to 350 degrees F.
  2. In a large mixing bowl, whisk together the flour and baking soda.
  3. In a separate bowl, mix together the melted butter, eggs, brown sugar and vanilla.
  4. Add the wet ingredients to the dry ingredients and mix until combined. Set aside for 15-20 minutes to allow the grains to soften.
  5. Prepare a 9x11 baking pan by greasing with butter.
  6. Mix the chocolate chips and nuts (if desired) into the bowl and spread the mixture into the 9x11 baking pan.
  7. Bake at 350 degrees F for 20-25 min, until edges are lightly browned. Note: You don't want to over-bake, but take them out just before you think they're done!

You might also like:

Whole Wheat Bread (made with fresh milled flour)

Healthy Oatmeal Spelt Cookies

Impossible Coconut Custard Pie (with fresh milled flour)

Whole Grain Maple Cinnamon Donuts

Fresh Milled Flour Dinner Rolls

Light & Fluffy FMF Waffles

Pan of whole wheat blondies fresh from oven, with text overlay "Healthy, chewy whole wheat blondies"

8 thoughts on “Whole Wheat Chocolate Chip Cookie Bars”

  1. In the ingredients you list baking powder but in the instructions you say to mix the flour and baking soda together. Curious which is correct?

  2. So there is NO Baking powder in this recipe? usually soda & powder? Making sure. I spread my last choc ship cookie recipe on parchment paper in my baking sheet and baked about 18 min and was delicious. Making sure there is really NO baking powder in this recipe?

  3. This is my very first dessert with freshly milled flour! It was very, very gooey at the time, but the top is browned. What hint do I need?

    1. Was it still gooey after it cooled? It may depend on the type of baking pan used, but some have found it needs more baking time. This one can be a tad tricky because if you brown it very much, it will become hard pretty fast after cooling. Hopefully you found the right balance (or will, after making it a 2nd time.) 🙂

  4. Have made these twice and they are so good! I use a 9×9 baker, as I don’t have a 9×11. they are probably thicker, but come out great baked for 25 minutes. For those who measure by weight, I used 315 g of soft white wheat. Thanks for sharing!

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