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!

whole wheat peanut butter cookies pin image

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 whole grain goodness?

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

a peanut butter cookie with whole wheat flour broken in half to expose the chopped peanuts

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.

You might also like to try my Whole Wheat Molasses Cookies.

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.

a stack of whole wheat peanut butter cookies

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.

a mixture of hard white and soft white wheat berries to make into freshly milled flour

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.

close up view of a whole wheat peanut butter cookie with natural peanut butter

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.
soft and chewy peanut butter cookie dough

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.

pressing the whole wheat peanut butter cookies with the tines of a fork

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.

whole wheat peanut butter cookies on a piece of white parchment paper

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!

Follow me on Instagram @aberlehome and tag me on your photo to show me what you made!

whole wheat peanut butter cookies

Whole Wheat Peanut Butter Cookies

Yield: about 2 dozen cookies
Prep Time: 30 minutes
Cook Time: 16 minutes
Total Time: 46 minutes

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


  • 85g whole wheat flour (or freshly-milled hard white or red wheat berries)
  • 95g whole wheat pastry flour (or freshly-milled soft white wheat berries)
  • ½ teaspoon baking soda
  • 10g (1 Tbls) cornstarch (or sub with 10g additional flour)
  • 1/8 teaspoon kosher salt
  • 115g (½ cup) salted butter, softened
  • 157g natural creamy peanut butter, well stirred (not processed peanut butter)
  • 80g light or dark brown sugar
  • 105g granulated sugar
  • 1 large egg + 1 egg yolk
  • 1 teaspoon pure vanilla extract
  • 70g lightly salted dry roasted peanuts, coarsely chopped


  1. Preheat oven to 375°F (350°F convection).
  2. Mix Cookie Dough: In a medium-size bowl, whisk together flours, baking soda, cornstarch, and salt until well combined. Set aside.
  3. In a large bowl with an electric mixer or in the bowl of a stand mixer fitted with a paddle attachment, beat together softened butter, natural peanut butter, brown sugar, and granulated sugar on high speed for one minute until creamy.
  4. Add in the egg and extra yolk and vanilla extract. Mix on medium-high speed until combined, scraping down the sides and bottom of the bowl as necessary.
  5. Add reserved dry ingredients and mix on low speed until just combined. Finally, fold in peanuts with a spoon or rubber spatula.
  6. Scoop cookies: Line a half sheet pan with parchment paper. Use a cookie scoop or spoon to drop 2 tablespoons of dough onto the pan for each cookie. Space 12 on the pan evenly. Press a criss-cross pattern in the top of each cookie with the tines of a fork to flatten the cookies slightly.
  7. Bake: Bake on the center rack for 8 minutes (or stagger multiple trays on racks if baking in a convection oven). Cookies will not turn golden brown when done baking--they will still appear very soft, though not raw in the center.
  8. Allow cookies to cool on the pan for a few minutes, then use a spatula to transfer cookies to a wire rack to finish cooling. Repeat to bake remaining cookies, if necessary.


  • The brand of natural peanut butter used in this recipe is salted.
  • Altitude adjustment: I use only 1/3 teaspoon baking soda at 9,000ft elevation to prevent spreading. If you're at a low elevation, you may need to increase the baking soda slightly.
  • Freshly-milled flour: Weigh wheat berries prior to milling to make the exact amount of flour you need for the recipe. Mill on the finest setting.
  • Make ahead instructions: The finished dough balls can be chilled, if desired, and baked later or the next day. The cookies may take a minute or two longer to bake when cold. The dough balls can also be frozen after criss-crossing with a fork. Place in the fridge the day before baking to allow the cookies to thaw, then bake as normal.
  • How to store: Store cooled cookies in an airtight container for up to one week. For longer storage, freeze well-wrapped for up to three months.

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Nutrition Information:
Yield: 24 Serving Size: 1
Amount Per Serving: Calories: 170Total Fat: 8gSaturated Fat: 2gTrans Fat: 0gUnsaturated Fat: 5gCholesterol: 18mgSodium: 84mgCarbohydrates: 21gFiber: 2gSugar: 9gProtein: 5g

*Nutrition information is not always accurate.