Whole Wheat Peanut Butter Cookies

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Soft and chewy whole wheat peanut butter cookies with natural peanut butter and without shortening. A perfect recipe for freshly milled flour!

There’s nothing dense or dry about this whole wheat cookie recipe!

These peanut butter cookies taste just as good as cookies made with all-purpose flour, so why not squeeze in the healthy whole grain goodness?

Lightly salted, chunky peanuts pair so well with the soft and chewy texture of the cookies.

You’ll feel so good offering these to your family.

Cornstarch is an optional ingredient that further softens the texture of the cookies, but you can replace it with additional flour, if you prefer.

Baking Cookies with Freshly-Milled Whole Wheat Flour

Whether it’s cookies, waffles, or muffins, I personally love to use home ground flour for added nutrition and flavor.

Stoneground whole wheat flours don’t last as long as all-purpose flour. The flour will start to go rancid after 3 months.

For this reason, I find it convenient to store a variety of organic grains in their whole form to use at my leisure rather than storing bags of different flours from the store.

If you would like to learn how to mill your own flour at home, visit this beginner’s guide.

Many people prefer soft white wheat berries in cookies for a light texture. Soft white wheat is still a whole grain, but it has a lower protein content than regular hard wheat.

I find, though, that my cookies turn out a bit crumbly with 100% soft white wheat.

I prefer to use a combination of soft white wheat and hard wheat (either hard red wheat or hard white) for the perfect balance.

No worries if you don’t mill your own flour.

This recipe works great with store-bought whole wheat flours. Whole wheat pastry flour and whole wheat flour can be found in the baking isle at the grocery store.

Tips for Making Whole Wheat Peanut Butter Cookies

• The recipe is listed by weight for the best results. You’ll find it’s much easier to weigh sticky peanut butter than to try to measure it out! I link to my favorite scale in the recipe card, but any kitchen scale will work.
• This recipe is formulated for natural creamy peanut butter and hasn’t been tested with regular processed peanut butter. Make sure you stir your natural peanut butter well before you add it to the recipe.

How to Make Whole Wheat Peanut Butter Cookies (Step-by-Step Instructions)

Step 1 – Mix the Peanut Butter Cookie Dough

After you preheat your oven to 375°F (or 350°F convection), start by mixing your dry ingredients for the recipe.

You’ll be whisking together the whole wheat flours with baking soda, cornstarch, and salt. Set that mixture aside for now.

In another bowl, add the softened butter, peanut butter, brown sugar and granulated sugar.

Beat these ingredients together on high speed using either a stand mixer fitted with a cookie paddle or an electric hand mixer.

Keep beating for about a minute until the mixture looks nice and creamy. Scrape down the sides of the bowl as needed. Then add your egg and extra egg yolk and vanilla extract.

Beat on medium-high speed now to combine. Finally, add in the reserved dry ingredients and beat on low speed until your whole wheat peanut butter cookie dough comes together.

Fold in coarsely chopped peanuts at the very end. You won’t want to use your mixer for the peanuts.

Step 2 – Scoop the Peanut Butter Cookies

I like to use a standard cookie scoop (2 tablespoons) to scoop out the cookies onto a half sheet pan lined with parchment paper. Evenly space 12 cookies on one pan.

If you don’t own a cookie scoop, simply drop them on with a spoon and form them into a ball with your hands.

Use the tines of a fork to press a criss-cross pattern into each cookie.

Step 3 – Bake the Peanut Butter Whole Wheat Cookies

Bake one tray of cookies at a time on the center rack (or stagger multiple trays on the racks if using a convection oven) for 8 minutes.

The peanut butter cookies will have a soft appearance when they are done, but will not turn golden brown!

The trick to making soft and chewy peanut butter cookies is getting the baking time right if your oven runs cooler or hotter. If you go too long, the cookies will be more on the crunchy side.

Leave the baked cookies on the tray for a couple of minutes before transferring them to a cooling rack to cool completely.

Repeat to bake the remaining cookies, if needed.

Make Ahead Instructions

You can certainly chill the dough balls before you bake them if you want to make the batter ahead of time or even the day before. You’ll likely need to increase the baking time by 1 minute.

You can even freeze the cookie dough balls in an airtight container after pressing them with the fork. Put them in the fridge overnight to thaw and bake them the next day.

How to Store Whole Wheat Peanut Butter Cookies

Peanut butter cookies with whole wheat flour store well in an airtight container at room temperature for about a week. I think they taste the most fresh through day 3.

You can freeze cookies for longer storage (up to three months if wrapped well) and leave them at room temperature to thaw when you are ready to consume them.

If you make this recipe and love it, I would be so grateful if you would come back to leave a star rating and a comment. Your feedback is very appreciated!

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