These are the ultimate whole wheat chocolate chip cookies! They're moist and chewy in the center, with crispy edges, and incredible flavor. They're easy to make from scratch with simple ingredients, and they're ready in just 55 minutes!

If you're a chocolate chip cookie lover, you'll also enjoy our miso chocolate chip cookies, sea salt and brown butter chocolate chip cookies, and egg-free chocolate chip cookies.

A spatula lifting a Whole Wheat Chocolate Chip Cookie off of a pan.

This whole wheat chocolate chip cookie recipe is a winner in our kitchen. They've got the taste and chewy texture we're after, with just the right amount of golden crunch around the edges, and lots of melty chocolate chips.

The whole wheat flour doesn't just make these cookies healthier, it actually gives them another dimension of flavor. It results in a substantial cookie that's both tender and toothsome.

It's a good, simple recipe that you can come back to again and again, and most of the ingredients you're likely to have in your kitchen already.

To make them, cream the butter with the sugars, then add in the egg and vanilla. Whisk the dry ingredients together, add them to the wet, and then fold in the chocolate chips. Let the cookie dough chill in the fridge for about a half hour before you pop the cookies into the oven.

They're the perfect anytime cookie to satisfy a sweet tooth, and they freeze beautifully so you can have freshly baked cookies whenever life calls for them!

Whole wheat flour vs all-purpose flour

Whole wheat flour contains the outermost shell of the wheat kernel, making it a denser flour. It results in a cookie with a deeper flavor, that's hearty but still tender. All-purpose flour is separated from the bran during the milling process, so it has a lighter texture.

The outer shell of the wheat kernel is full of fiber, and it contains a large percentage of the vitamins and minerals. This is what makes whole wheat flour a more nutritious and flavorful choice!

A close up of a plate of whole wheat cookies with chocolate chips.

One of the (many) things we love about chocolate chip cookies, is that we always seem to have the ingredients to make them in our kitchen. Here's everything you need to make this whole wheat cookie recipe:

  • Butter – we use salted butter to give these cookies richness, tenderness, and structure like no other. You can also use unsalted butter, but add in a ¼ teaspoon more salt.
  • Brown sugar and granulated sugar – a mix of brown sugar and granulated sugar makes these cookies taste sweet while keeping them moist and chewy.
  • Vanilla extract – pure vanilla extract has its own distinct warm flavor, and it actually acts as a flavor enhancer as well.
  • Whole wheat flour – whole wheat flour makes these cookies heartier, and healthier too!
  • Egg, baking powder, and salt – traditional cookie ingredients to bind, rise, and flavor.
  • Chocolate chips – we like either dark chocolate chips, or semi-sweet chocolate chips, but any type of chocolate chips work.

How to make whole wheat chocolate chip cookies

You don't need a special occasion to enjoy a whole grain chocolate chip cookie. They're a delicious anytime treat that everyone loves! Here's how we make them in a couple of easy steps:

  1. While your oven preheats, soften the butter in the microwave. It should be nice and soft, but not entirely melted.
  2. Beat both sugars with the butter, then add in the egg and vanilla.
  3. Whisk the dry ingredients together, stir them into the wet ingredients until just combined, and then fold in the chocolate chips.
  4. Scoop and roll the dough into balls, place them on a baking sheet, and then refrigerate them for at least 30 minutes. This makes the cookies more flavorful and prevents them from spreading too much.
  5. Bake the cookies until they've puffed up and just started to brown. Allow them to cool slightly before transferring them to a cooling rack.

Full recipe instructions are in the recipe card below.

A hand holding a chocolate chip whole wheat cookie with a bite out of it.

If you want to freeze the cookie dough, it's easy to do in a few simple steps:

  • Prepare the cookie dough per the recipe instructions.
  • Scoop the cookie dough into individual cookies onto a baking sheet lined with parchment paper or a silicone mat.
  • Place the baking sheet in the freezer for about an hour.
  • Once they're firm, transfer them to a container or reusable bag.
  • Freeze them for up to 3 months!
  • Thaw at room temperature when ready to use.


Can I freeze them?

Absolutely! You can either freeze the cookie dough, or the cookies once they're baked. Both the dough and cookies will freeze for 3 months!

Can I use all-purpose flour instead?

We've only tested this recipe with whole wheat flour which tends to be denser than all-purpose flour, so we can't guarantee the results.

Can I make them without an electric mixer?

You can definitely mix the wet ingredients without an electric mixer, but it will take some elbow grease. Use a wire whisk or a wooden spoon to beat the ingredients until they're well combined.

Why do you refrigerate the dough?

Chilling the dough is an important step that we don't recommend skipping. When making the dough, the butter becomes warm, and chilling it helps the cookies keep their structure, and stops them from spreading. It also let's the flavors develop so you'll get a tastier cookie.

How do you know when the cookies are done?

We tend to slightly under-bake these cookies so they come out soft and chewy. They bake quickly in 8-10 minutes, but since all ovens vary slightly, take them out when they start to have golden edges. They will look underdone at first, but they will firm up as they cool.

The perfect chocolate chip cookies for any occasion

These whole wheat flour chocolate chip cookies are exactly what we're after when we're craving a classic cookie. Enjoy them with a glass of milk, a cup of coffee or tea, or a creamy almond butter latte.

Tuck them into school lunch boxes, wrap them up and share them with friends, or take them on a hike as delicious fuel. They'll bring smiles to faces of both kids and adults, and it's always the right time for a chocolate chip cookie!

Whole Wheat Chocolate Chip Cookies on a plate next to a glass of milk.
Looking down on a plate of Whole Wheat Chocolate Chip Cookies.

Whole Wheat Chocolate Chip Cookies

These are the ultimate whole wheat chocolate chip cookies! They're moist and chewy in the center, with crispy edges, and incredible flavor. They're easy to make from scratch with simple ingredients, and they're ready in just 55 minutes!

If you love this recipe as much as we do, let us know with a 5-star rating!

5 stars (35 ratings)
Print Recipe Rate Recipe Pin Recipe


  • ½ cup salted butter, softened
  • ½ cup granulated sugar
  • ¼ cup brown sugar
  • 1 tablespoon vanilla
  • 1 large egg
  • 1 ½ cups whole wheat flour
  • ½ teaspoon baking powder
  • ¼ teaspoon salt
  • ½ cup chocolate chips, plus a few extra on top


  • Line a baking sheet with parchment paper. Put the butter into a large bowl and microwave it for 30 seconds – see notes.
    ½ cup salted butter
    image for recipe instruction
  • Add both the sugars to the butter and beat with electric beaters for 1 minute. Mix in the egg and vanilla.
    ½ cup granulated sugar, ¼ cup brown sugar, 1 tablespoon vanilla, 1 large egg
    image for recipe instruction
  • In a medium-sized bowl, whisk the flour, baking powder, and salt. Add this to the wet ingredients and mix just until it's combined – do not overmix. Fold in the chocolate chips.
    1 ½ cups whole wheat flour, ½ teaspoon baking powder, ¼ teaspoon salt, ½ cup chocolate chips
    image for recipe instruction
  • Roll 12 balls of dough and place them on the baking sheet – see notes. Press a few extra chocolate chips onto the top, if you'd like. Put the baking sheet into your fridge for half an hour.
    image for recipe instruction
  • Preheat your oven to 350 degrees. Put the chilled cookies into your oven and bake for 8-10 minutes, or until puffed up and ever so slightly starting to color. Let them cool for 10 minutes before moving them to a cooling rack.
    image for recipe instruction


The butter should be nice and soft, but not completely melted. The time it needs in the microwave will depend on how soft it is to start. Room-temperature butter needs 25-30 seconds to soften while butter from the fridge will take 40-45 seconds. See the picture to know exactly what the butter should look like!
Unless your baking sheet is very dark, you don't need to line it with parchment paper. We do as our pans are well-used and not the prettiest to look at.
Serving: 1 cookie, Calories: 177kcal, Carbohydrates: 24g, Protein: 3g, Fat: 8g, Saturated Fat: 5g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.3g, Cholesterol: 36mg, Sodium: 135mg, Potassium: 70mg, Fiber: 2g, Sugar: 13g, Vitamin A: 260IU, Calcium: 24mg, Iron: 1mg
DID YOU MAKE THIS RECIPE?If you love this recipe as much as we do, be sure to leave a review or share it on Instagram and tag @TheEndlessMeal.