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healthy chocolate chip cookies stacked on a cutting board, with one cookie broken for a closeup inside and milk in the background
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5 from 9 votes

Secretly Healthy Chocolate Chip Cookies

Sinking your teeth into one of these healthy chocolate chip cookies is so satisfying and delicious. With only 100 calories per cookie, they are sweet, chewy, and the perfect dessert for all occasions! 
Prep Time49 mins
Cook Time11 mins
Total Time1 hr
Course: Baking, Dessert
Cuisine: American
Servings: 60 cookies (5 dozen)
Calories: 106kcal
Author: Anjali Shah


  • cups whole wheat flour or whole wheat pastry flour
  • ¾ cup lentil flour mixes best at room temperature, not cold
  • 1 tsp salt
  • 1 tsp baking soda
  • 1 cup butter softened (note - the 1 cup of butter is a lot, but among the serving size - 60 cookies, it amounts to only about 15 calories of butter per cookie)
  • ¾ cup coconut sugar
  • ¾ cup packed brown sugar
  • 2 large eggs
  • 1 tsp vanilla extract
  • 2 tbsp agave nectar
  • cups chocolate chips you can change this up and add peanut butter or butterscotch chips if you like!
  • ½ cup chopped nuts


  • Preheat oven to 350 degrees.
  • Combine flours, salt and baking soda in a small bowl.
  • Beat butter, sugars and vanilla extract in a large mixing bowl until creamy.
  • Add eggs and syrup, beating well.
  • Gradually beat in flour mixture.
  • Stir in chocolate chips and nuts.
  • Drop by rounded tablespoons onto ungreased baking sheets.
  • Bake 9 – 11 minutes or until brown.


Top Tips For Making The Best Healthy Chocolate Chip Cookies
  • Never overmix the batter. If you do overmix the batter your cookies will be dense and won’t taste near as good. Plus, when you overmix cookie dough it causes air bubbles to form - so when the cookies are baked the air bubbles pop and it leads to flat, super crispy (not soft/chewy) cookies.
  • Don’t grease your baking sheet or the cookies will not turn out well. Because of the butter in the cookies they will already have enough oil. 
  • The lentil flour mixes best at room temperature, not cold
  • Make sure to use softened butter, not melted butter in this recipe as it will change the texture of the cookies.
  • When scooping the cookies, be sure to pack them tightly in the cookie scoop/spoon so that they don't fall apart in the oven
  • Make sure your baking soda is fresh (not expired!) so that your cookies rise properly and aren't too flat.
  • When measuring the flour, be sure to spoon and level it into your measuring cup (vs. scooping the flour out with your measuring cup). That will ensure you end up with light cookies that aren't too dense.
  • To reduce the sugar even more, use 1/2 cup coconut sugar + 1/2 cup brown sugar in this healthy cookie recipe
  • Let the cookies cool completely before serving.


Serving: 1cookie | Calories: 106kcal | Carbohydrates: 14g | Protein: 1.2g | Fat: 5.9g | Sodium: 42.9mg | Fiber: 0.5g | Sugar: 10.5g