The Best Healthier Chocolate Chip Cookies

Soft, chewy, melt-in-your mouth chocolate chip cookies. Bonus? They are healthier than your average cookie. Sweetened with coconut sugar and completely gluten-free and vegan.

the best healthier chocolate chip cookies

I set up a task to make a new favorite chocolate chip cookie that was both gluten-free and vegan. Now, that combo is sort of difficult when it comes to cookies. You don’t want it too dry and you don’t want it too soft.

These cookies are a dream. With a soft, chewy center and slightly crispy edges. They have rich dark chocolate pools and hints of molasses. Not to mention, they contain simple ingredients and are super easy to make.

the best healthier chocolate chip cookies

I’ve found that a 1-1 ratio of oat flour and almond flour makes for the perfect texture and taste. To add extra chewiness I added 1 tbsp of molasses which provides that perfectly soft center.

What exactly makes these The Best Healthier Chocolate Chip Cookies? Let’s break down some of the ingredients:

the best healthier chocolate chip cookies

Softened coconut oil: A healthier substitute for vegan butter (which is typically in cookies) is softened coconut oil! I recommend using refined coconut oil, as it will have less of a coconut flavor than unrefined. Why softened coconut oil? Let’s discuss the use of softened butter first then you’ll understand how coconut oil works similarly.

When making cookies, you want to first cream together the butter and sugar. When it’s softened it’s easier to whip it and obtain a creamy texture.

Also, the structure of softened butter will yield a fluffy, but chewy cookie. As the butter melts in the oven it will cause the cookie to flatten, but not flatten as much as if you were to use melted butter. If you were to use cooled butter, the cookie would hold its shape more when baked. Get the gist? That’s how this softened coconut oil will work.

Coconut sugar + molasses: Most cookie recipes will call for brown sugar and there are two common reasons for this. One: it will aid in a golden brown cookie. Two: brown sugar contains molasses which is an invert syrup. Invert syrups are very hygroscopic. Hygroscopic means it will attract and absorb more liquid. This will cause your final product to be more chewy and moist.

Coconut sugar is a great healthier alternative to brown sugar, but the addition of molasses will lend you to not sacrifice that chewy, moist texture that brown sugar adds!

the best healthier chocolate chip cookies

Almond flour + oat flour: I have tested and tried multiple gluten-free flour variations in a plethora of baked goods, and I have found that this is by far my favorite. The nuttiness of almond flour adds a delicious taste to the cookies.

Also, these two flours combined makes for a perfectly fluffy cookie that won’t fall apart on you (if combined with the right ingredients of course).

Baking soda: Going back to molasses, it is also acidic. Baking soda is alkaline which means it has a high pH. When combined with an acidic ingredient, such as molasses, it will cause the baked goods to rise.

Although we don’t want a cakey, bread-like cookie, we still want those babies to rise! That is where this combination of baking soda and molasses comes in.

If you would like to read more about the functions of baking soda and baking powder in baked goods I recommend this article by Sally’s Baking Addiction.

Dark chocolate chunks: I’ve stressed this so many times in countless recipes, but the chocolate you use in your baked goods will make a difference in the taste of your product! I recommend a good quality dark chocolate, specifically a chocolate bar. It will yield gooey, melty pools of chocolate that we all love.

the best healthier chocolate chip cookies
the best healthier chocolate chip cookies

These Healthier Chocolate Chip Cookies are…

  • Soft
  • Chewy
  • Crispy
  • Easy
  • Simple
  • Gluten-free
  • Vegan

3.86 from 7 votes
healthier chocolate chip cookies
The Best Healthier Chocolate Chip Cookies
Prep Time
10 mins
Cook Time
15 mins
Total Time
25 mins

Soft, chewy, melt-in-your mouth chocolate chip cookies. Bonus? They are healthier than your average cookie. Sweetened with coconut sugar and completely gluten-free and vegan.

Course: Dessert
Keyword: gluten-free, paleo, vegan
Servings: 12 cookies
Author: Taavi Moore
  • 1 tbsp flax seed meal or sub chia seed meal
  • 2 tbsp water
  • cup softened coconut oil*
  • ½ cup coconut sugar
  • 2 tbsp non-dairy milk
  • 1 tbsp molasses*
  • 1 tsp vanilla extract
  • 1 cup almond flour
  • 1 cup oat flour
  • ½ tsp baking soda
  • ½ tsp baking powder
  • ¼ tsp sea salt
  • ½ cup chocolate chunks or chopped dark chocolate
  1. Preheat the oven to 375 degrees (trust me, this higher temperature makes a difference). Line a baking sheet with a silicone baking mat or parchment paper. To a small bowl, whisk together flax seed meal and water. Set aside for 5 min.

  2. In a large mixing bowl using a handheld mixer, cream together softened coconut oil, flax egg, coconut sugar, milk, molasses, and vanilla until creamy. Add flours, baking soda and powder, and salt. Using a spatula or wooden spoon, combine mixture until a soft dough forms. Fold in chocolate chunks.

  3. Using a small cookie scoop, evenly portion dough on to the baking sheet. Slightly press down each cookie with the palm of your hands. Bake for 12-15 min. until light golden brown. Let cool for 10 min. before transferring to a wire cooling rack (important!).

Recipe Notes

*To achieve the best consistency for softened coconut oil in this recipe, let your coconut oil sit at room temp for about an hour. Depending on you surrounding temp you may need to microwave it for 10-15 sec. You just don’t want it to melt. 

*Brown rice syrup has been tested and works as an alternative to molasses if you don’t have any on hand. Any invert syrup should work as a substitution! 


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