Chocolate Chip Flax Seed Cookies

My kids spent the weekend watching Star Trek. My husband decided it’s required viewing…important social commentary or something. He’s a Trekkie and I didn’t know it. And actively recruiting.

So while they watched 3 movies, select episodes of the original series (Daddy “that doesn’t even look real”) and then started Enterprise from.the.beginning, (thank-you Netflix!) I’ve been busy in the kitchen making cookies.

Looking for a cookie you can feel good about sending in your kids lunch? A cookie that the kids will be happy to eat even?

This might be it. They are made with whole wheat flour, a bunch of flax seeds (a full cup in total) and oats. I added chocolate chips, because a cookie isn’t a cookie without chocolate chips. In my opinion, anyway.

Chocolate Chip Flax Seed Cookies

Soaking the flax seeds in the milk  before baking softens the seeds and thickens the milk they sit in. Think chia seeds, you will get the same jelly like custard after soaking, it just takes longer. Soaking in acidic milk (I used soy milk curdled with apple cider vinegar) takes away some of that “flax-y” taste as well. You will  need to plan ahead for this, it is best if the seeds soak for about 2 hours. 

Dark chocolate chips and sunflower seeds make for an interesting and happy cookie. A cookie that tastes like a treat.  Without negating the other healthy ingredients you’ve added in. Feel free to substitute whatever nuts or dried fruit you like. I wanted these for the kids lunch boxes so I couldn’t use nuts. And my kids are not crazy about dried fruit.

I find these cookies rather perishable. They will keep on the counter only for a couple of days. For longer storage you will need to stick them the in fridge or freezer. I’ve tried both, they keep in refrigerator for about 5 days and they freeze beautifully.

Tip: wrap them individually in plastic wrap before stuffing in the freezer and you will lunchbox ready treats!

You will get about 36 cookies per batch, a generous sized cookie. They are quite filling and hearty, one will do.

Chocolate Chip Flax Seed Cookies


Chocolate Chip Flax Cookies

Servings: 36 cookies


  • 1/2 cup whole flax seeds
  • 1-1/2 cups curdled milk buttermilk or 1 tablespoon vinegar + milk to fill to 1-1/2 cups, I used soy mlik
  • 2 cups whole wheat flour
  • 1/2 cup ground flax seeds
  • 1 cup rolled large flake oats
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon sea salt
  • 1 teaspoon cinnamon
  • 1/2 teaspoon ground nutmeg
  • 1 cup grapeseed oil or other mild tasting vegetable oil
  • 1 cup brown sugar
  • 2 eggs
  • 2 tablespoons vanilla extract
  • 2 cups sunflower seeds or almonds, or other nuts
  • 1/2 cup dark chocolate chips or dried fruit


  • In a medium sized bowl, place whole flax seeds in 1-1/2 cups of curdled milk and set aside for about 2 hours at room temperature.
  • Preheat oven to 350 and line 2 cookie trays with parchment paper.
  • In a large bowl mix together flour, oats, ground flax seeds, baking powder, baking soda, salt, cinnamon and nutmeg.
  • To the milk and whole flax seed mixture add the oil, vanilla, eggs and brown sugar. Beat well to combine to a creamy consistency.
  • Add wet ingredients to the dry and fold together until just combined. Fold in seeds and chocolate chips.
  • Drop large - 2 tablespoon sized cookies - onto the parchment lined baking sheets, about 2 inches apart. Bake at 350 for about 15 minutes.