Chocolate Chip Flax Cookies

Chocolate Chip Flax Cookies

I make these Chocolate Chip Flax Cookies regularly for a healthy snack for my kids. They take these nut-free cookies in their lunch boxes to school every day. Adults and kids alike enjoy these healthy chocolate chip flax cookies despite the atypical ingredients.

Some of my recipes I create completely from scratch and many, like this one, I modify from an existing recipe to create a healthier version. While you might argue that there is no such thing as healthy chocolate chip cookies, I would say these are at least healthier than regular chocolate chip cookies.

Chocolate chip cookies on wooden cutting board on green table

Here are the ingredients that I modified to make my chocolate chip flax cookies healthier than regular chocolate chip cookies.

Healthy Baking Substitutions Chart

Non-hydrogenated margarine – based on the most recent data, non-hydrogenated fats appear better for the blood lipid levels than saturated animal fats (e.g. butter). Most chocolate chip cookie recipes will use butter.

Coconut Palm Sugar – a glycemic index of 35 and a fructose level of 9% is the reason I choose this sugar. I do think reducing the amount of added sugar in the diet is the first step though, which is something I also did for this recipe. Most chocolate chip recipes will use a combination of white and brown sugar in larger amounts.

Omega-3 eggs – Omega-3 is anti-inflammatory and I look to include it wherever I can. Most chocolate chip recipes won’t specify omega-3 eggs, but it’s an easy substitution to make.

Real Vanilla – contains beneficial plant compounds including vanillin. Most chocolate chip cookie recipes will use real  or artificial vanilla, both contain vanillin, but real vanilla contains other beneficial nutraceuticals as well.

Barley flour – contains beta glucans, which are supportive of the immune system, it’s also a whole grain and substitutes 1:1 for white flour in recipes. Most chocolate chip cookie recipes use white flour, some healthier recipes may include a combination of white and whole wheat flour.

Ground flax seeds – the lignans, fiber and omega-3 fatty acid are the reason I add ground flax seeds. Most chocolate chip cookie recipes won’t contain any ground flax seeds. I like adding these to all my baking.

70% coco chocolate chips – the darker the chocolate, the higher the polyphenol (beneficial plant compound) content and the less sugar. Most chocolate chip cookie recipes will use milk or semi-sweet chocolate chips.

Chocolate Chip Flax Cookies

Prep Time40 d
Cook Time12 mins
resting time10 mins
Total Time50 mins
Course: Snack
Cuisine: American
Keyword: barley, chocolate chip, cookies, flax, healthy cookies, immune boosting, kid-friendly, nut-free
Servings: 40 Cookies
Author: Jean LaMantia


  • mixing bowls
  • hand or stand mixer
  • measuring cups and spoons
  • cookie sheet/sheet pan
  • parchment paper
  • number 40 scoop


  • 1 cup non-hydrogenated margarine
  • 1 1/2 cup coconut palm sugar
  • 3 x omega-3 eggs
  • 3 tsp pure vanilla extract
  • 3 3/4 cups barley flour
  • 1 1/2 tsp baking soda
  • 3/4 cup ground flax seeds
  • 3/4 cup 70% coco chocolate chips


  • Preheat the oven to 375 F
  • In a medium bowl, cream the margarine. Beat in the coconut palm sugar until fluffy. Do not over beat.
  • Add the eggs and vanilla. Beat briefly, until mixed.
  • In another bowl, mix the barley flour, baking soda and ground flax seeds.
  • Beat the dry ingredients and wet ingredients together until blended. Use a rubber spatula to scrape the bowl and make sure ingredients are mixed uniformly.
  • Add the chocolate chips and beat briefly until mixed in.
  • Drop by size 40 scoop onto cookie sheet lined with parchment paper
  • Bake for 12 minutes until bottom of cookie is lightly browned. When you cook with barley flour, the cookies don’t darken as much as with all purpose flour.


While barley flour will substitute 1:1 with all purpose flour, I find it doesn't brown the same way. Keep this in mind when you are checking the cookies. These cookies freeze well. 

With this recipe and a size 40 scoop, I get 40 cookies on my sheet.

40 chocolate chip flax cookies on sheet pan      size 40 scoop


Making modifications to recipes is one way that you can make positive changes to your diet to help improve your intake of beneficial ingredients. If you would like to work with me one-on-one to determine the best way to improve your favourite comfort food recipes, then please get in touch at

The cookies will expand a bit during baking, but will retain the shape of the scoop.

Finished chocolate chip flax cookies on sheet

Here are some of the brands that I use to create my chocolate chip flax cookies

chocolate chip flax cookies with ingredients

  • Pure Palm coconut palm sugar
  • Cocoa Camino 70% chocolate chips
  • Simply Organics Vanilla
  • Mountain Path barley flour
  • Becel vegan margarine (not pictured)

If you like this recipe, be sure to check out my Festive and Healthy Nut Loaf

Please let me know your comments, especially if you tried the recipe.


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