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5 from 1 vote

Whole Wheat Chocolate Chip Cookies

Whole Wheat Chocolate Chip Cookies are soft and chewy in the middle with slightly crispy edges and lots of melty chocolate chips. This healthier twist on a classic is easy to make and has a delicious nutty flavor that will bring you back for seconds - or thirds! Adapted from the cookbook Good to the Grain.
Prep Time10 mins
Cook Time10 mins
Total Time20 mins
Course: Dessert
Cuisine: American
Servings: 24 cookies
Calories: 336kcal


  • Cookie sheet
  • Parchment paper (or silicone baking mat)
  • Mixing bowls
  • Electric mixer
  • Cookie scoop (optional)


  • 3 cups (339 g) whole wheat flour
  • 1 tsp baking soda
  • tsp baking powder
  • tsp kosher salt
  • 1 cup (2 sticks, 226 g) unsalted butter softened
  • 1/2 cup (99 g) granulated white sugar
  • 1 1/2 cups (320 g) light brown sugar
  • 2 tsp vanilla extract
  • 2 large eggs room temperature
  • 2 cups (12 oz, 340 g) semi-sweet chocolate chips


  • Preheat the oven to 350° F. Line two cookie sheets with parchment paper (or a silicone baking mat). 
  • Sift together flour, baking soda, baking powder and salt in a medium bowl. Set aside.
  • With an electric mixer, beat butter, granulated sugar, and brown sugar on medium high until light and fluffy, about 2 minutes. Use a spatula scrape down the bowl. 
  • Add eggs, one at a time, beating well after each addition. Add vanilla and mix just until combined. 
  • Add dry ingredients all at once and mix on low until just combined. Stir in chocolate chips. 
  • Using a 1-inch cookie scoop or a tablespoon scoop the cookies into 1 ½ inch balls onto prepared cookie sheets about 2 inches apart. 
  • Bake cookie sheet on the middle rack for 12-14 minutes, until lightly browned on the sides. The centers will still look soft.  Remove from the oven and let cool on a baking sheet for 5 minutes before transferring to a wire rack to cool completely.  


  • Measure flour carefully. Whole wheat flour is more dense than white flour, so you don’t want to overmeasure. Use a kitchen scale for exact measurements, or use a spoon to scoop the flour into the measuring cup and level it off with a butter knife. Don’t pack the flour down. 
  • Soften your butter correctly. The butter should be softened to room temperature, which means you can slightly indent your thumb into the butter but shouldn’t easily smoosh all the way through. 
  • Don’t overmix. As with all baking recipes, overmixing causes tough, dense dough. Mix until just combined.
  • Don’t overbake. For that signature soft, chewy center with slightly crispy edges, you can’t bake the cookies too long. The centers should still look slightly soft when you take them out of the oven. They will continue cooking slightly on the cookie sheet.
  • Storage: Can be stored in an air-tight container at room temperature for up to 3 days. 


Calories: 336kcal | Carbohydrates: 43g | Protein: 4g | Fat: 17g | Saturated Fat: 10g | Cholesterol: 44mg | Sodium: 251mg | Potassium: 230mg | Fiber: 3g | Sugar: 27g | Vitamin A: 320IU | Calcium: 48mg | Iron: 2mg