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Whole Wheat Chocolate Chip Peanut Butter Cookie Recipe

Homemade chocolate chip peanut butter cookies – they are so so good, and not too hard to make a little healthier!

I love dessert, and I love chocolate and peanut butter anything (like this homemade freezer treat!). I also love real food.

So we make this delicious chocolate chip peanut butter cookie with whole grains (even low-gluten!), natural sweeteners, and even dairy-free options if you need them. This is one of my favorite peanut butter cookie recipes.

Healthy Whole Wheat Peanut Butter Cookies

I love a good chewy cookie. But whole grain, naturally sweetened cookies can be dry, crumbly, and not very flavorful. Not so with this cookie recipe. It is chewy, sweet, and yummy.

chocolate chip peanut butter cookies

Here’s how we made these cookies a little healthier:

Whole Wheat Flour

I’ve talked about this before, but I don’t usually use store-bought whole-wheat flour when I make cookies. The flour is too dense, it’s stale from sitting on the shelf forever, and it just doesn’t taste very good.

However, freshly ground whole wheat flour makes pretty decent cookies. Dare I say, delicious, homemade, better-for-you cookies?

While owning a flour grinder isn’t for everyone, I found that the cost savings and quality of our homemade whole-grain baked goods were worth the investment.

I’ve had my grain mill for 12 years and it paid for itself a long time ago! Go here to learn more about my wheat grinder and how it works in our kitchen!

RELATED: Katie put freshly ground wheat to the test here!

I use spelt flour for these cookies because it is sweet and nutty and doesn’t have a lot of gluten in it, which is better for our family. Otherwise, I recommend soft white whole wheat berries for this recipe.

If you do not have a flour grinder, try using just half whole wheat flour and half unbleached white flour.

Healthy Fats

No shortening here! Just butter. If you’re dairy-free, try this palm shortening that I use in other holiday cookies, like gingerbread, thumbprint cookies, and sugar cookies!

Natural Sweeteners

This recipe uses both sugar and maple syrup. Any kind of natural sugar works – turbinado, sucanat, or just plain old sugar. You are welcome to make it with all maple syrup using these instructions, but I found I like these cookies best with both maple syrup and sugar.

Peanut Butter

Ingredients should just include peanuts and salt.

chocolate chip peanut butter cookies

Chocolate Chip Peanut Butter Cookies Recipe

To make some of the best peanut butter cookies, simply mix the ingredients in the order in the recipe (I start by beating the peanut butter and butter together with an electric mixer), stir in the chocolate chips, and roll the spoonfuls of cookie dough into balls before placing them on the cookie sheet.

You then roll them in organic sugar, which is a delicious extra step for special occasions, but not necessary to make a good cookie.

To make these cookies ahead of time, freeze the balls of cookie dough on the cookie sheets, then transfer them to a freezer bag. This helps ensure you don’t eat the entire batch in one sitting, and you can bake just a few at a time as desired.

Freezing the dough instead of the fully baked cookies prevents crumbling in the freezer and maximizes those fresh home-baked cookie flavors.

Store finished cookies in an airtight container for up to 4 days (but honestly, they probably won’t last that long).

Healthy Peanut Butter Cookies

While I don’t love healthifying all desserts as a rule – if you’re gonna eat a cookie, eat a cookie – I do like to adjust our recipes to accommodate special diets and to feeling our best.

The truth is, I feel better after eating a better-for-me cookie than I do after eating one loaded with white flour and white sugar. I love the depth of flavor that comes from different kinds of sweeteners and whole grains.

It’s a different kind of cookie experience, but one that I would choose every time – as long as it’s still a good cookie. And these chocolate chip peanut butter cookies are good cookies.

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chocolate chip peanut butter cookies

Whole Wheat Chocolate Chip Peanut Butter Cookie Recipe

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  • Author: Stephani Jenkins
  • Prep Time: 15 minutes
  • Cook Time: 12 minutes
  • Total Time: 27 minutes
  • Yield: 3 dozen 1x
  • Category: Dessert
  • Method: Baked


Homemade chocolate chip peanut butter cookies – they are so so good, and not too hard to make a little healthier!


Units Scale
  • 3/4 c. natural peanut butter
  • 1/2 c. (1 stick) butter
  • 1/3 c. sugar (turbinado and other natural granulated sweeteners work great)
  • 2/3 c. maple syrup
  • 1 egg
  • 3 Tbs. milk
  • 1 tsp. vanilla extract
  • 3 c. whole wheat flour (I like spelt best)
  • 1 tsp. baking soda
  • 1/2 tsp. salt (Use the code kitchenstewardship for 15% off of your first purchase)
  • 1 1/2 c. chocolate chips
  • More granulated sugar, for rolling (optional)


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  1. Preheat your oven to 350 F.
  2. In the bowl of a mixer, beat together the peanut butter and butter. Beat in the sugar and maple syrup until the mixture is smooth and creamy. Add the egg and vanilla and beat until fluffy.
  3. In a separate bowl, combine the flour, baking soda, and salt. Slowly stir it into the peanut butter mixture until blended.  Stir in the chocolate chips.
  4. Roll the dough into 1-inch balls, then roll them in sugar (if using). Place them 1-inch apart on a cookie sheet.
  5. Bake for 10-12 minutes.
  6. Remove the cookie sheet from the oven, and let them cool for 3 minutes before using a spatula to move them to a cooling rack.


To Freeze: To make these cookies ahead of time, you can freeze the balls of cookie dough on a cookie sheet, then transfer them to a labeled freezer bag. When ready to bake, preheat the oven, then follow the baking instructions. You may need to bake them for 1-2 minutes longer.

To Store: Store cookies in an airtight container for up to 4 days.


  • Serving Size: 3 cookies
  • Calories: 469
  • Sugar: 28g
  • Sodium: 248mg
  • Fat: 23g
  • Saturated Fat: 11g
  • Trans Fat: 0g
  • Carbohydrates: 57g
  • Fiber: 3g
  • Protein: 11g
  • Cholesterol: 39mg

What is your favorite cookie recipe?

chocolate chip peanut butter cookie recipe
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