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Healthfully decadent 100% flax chocolate cookies ! Made in a muffin tin with only 5 ingredients, they are vegan, grain-free, oil-free, paleo and keto (with an ingredient swap).

Flax Breakfast Cookies get a Double Chocolate Boost
When I did a re-shoot of my popular 100% flax breakfast cookies last week, I realized I had made a terrible mistake.
I never created a chocolate version.
Here’s to: (1) making up for lost time, and (2) making 100% flax CHOCOLATE breakfast cookies for breakfast tomorrow (or a snack, right now)!
Recipe Benefits
Like my original version, these 100% flax chocolate cookies are:
- Vegan
- Grain-fee
- Oil-free
- Gluten-free
- Made with 5 ingredients
- Paleo
- Keto-friendly (with a simple ingredient swap)
Ingredients
The exact amounts of each ingredient are indicated in the recipe card at the end of the post. Toggle between US Customary (volume) and Metric (weights) for preferred measurement option.
- unsweetened natural nut butter or seed butter (e.g., almond butter, cashew butter, peanut butter, tahini or sunflower seed butter)
- coconut sugar (see notes for keto option and other options)
- unsweetened cocoa powder
- flaxseed meal
- miniature chocolate chips (see notes for keto option)
You will also need a small amount of boiling water to mix the dough. I like to add a pinch of salt (and, sometimes, a splash of vanilla extract, too). but it is optional.
Step by Step Instructions
Note that the complete directions are also in the recipe card below.
The cookies are super-simple to make, too. Yay!
- Preheat the oven to 325°F (160°C). Grease or spray the cups of a 12-cup muffin pan with nonstick cooking spray (no oil or spray is necessary if using a nonstick muffin tin / muffin pan).
- In a a medium bowl, combine the nut butter, coconut sugar, boiling water, cocoa powder and optional vanilla until blended and glossy. The boiling water helps to soften the nut butter and blend the ingredients into a glossy, harmonious, fudge-y base. You may want to stop right here, as this mixture is heavenly.

- Stir in the flaxseed meal (the mixture should be thick, but if it is especially stiff, add a little bit more water).

- Now you have a choice: stir 2 tablespoons of miniature chocolate chips directly into the dough, leave them out, or wait to sprinkle on top of the cookies.
- Once your choice is made, divide the batter between 12 greased or sprayed muffin cups. If you chose option #3, sprinkle the cookie tops with the chips.
- Bake in the preheated oven for 17 to 19 minutes until the surface of the cookies appears dry and the centers feel just firm to the touch.
- Let cool in pan on a wire rack for 10 minutes. Run knife around edges to loosen, then remove and place on rack to cool completely
Behold the chocolate goodness:

How Do the 100% Flax Cookies Taste?
The cookies have super-crispy edges, fudge-y middles, and intense chocolate flavor throughout, these are 100% delectable on top of being 100% flax.

How Should I Serve the Cookies?
- As a healthy breakfast on the go
- Pre- or post-workout snack
- Desseert
- Sweet, but energizing, treat with a midmorning or afternoon coffee

Happy baking!
FAQ
- How should I store the 100% flax chocolate breakfast cookies? Store the cooled cookies in an airtight container at room temperature 2 days, the refrigerator for 1 week, or the freezer for up to 6 months.
- How do I make the cookies nut-free? For nut-free cookies, use an equal amount of creamy seed butter (e.g. sunflower butter or tahini) in place of the nut butter.
- How do I make the cookie keto-friendly? Use an equal amount of keto-friendly granular sweetener in place of the coconut sugar. Leave out the chocolate chips or replace with sugar free chocolate chips.
- Keto macros per cookie without chocolate chips: [Calories: 77 / fat: 6.2 g/ sat. fat: 0.6 g/ carbohydrates:4.6 g / sugars: 1 g]
- Keto macros per cookie with sugar-free chocolate chips: [Calories: 88 / fat: 6.9 g/ sat. fat: 1.1 g/ carbohydrates:6.1 g / sugars: 1 g]
- What are some other options to replace coconut sugar? An equal amount of brown sugar or plain sugar can be used in place of the coconut sugar.
Related Recipes
- Almond Flour Flax Biscuits
- 2-Ingredient Flax Sandwich Bread
- Oat Flax Skillet Bread
- 100% Flax Breakfast Cookies
- 4-Ingredient Vegan Flax Muffins
- 2-Ingredient Quinoa Flax Bread
- 2-Ingredient Lentil Flax Bread
- White Bean Flax Biscuits

100% Flax Chocolate Cookies (V, GF, Oil-free)
Equipment
- standard size muffin tin (12-count)
Ingredients
- 1/2 cup unsweetened natural nut butter (e.g., almond, cashew, peanut)
- 1/3 cup coconut sugar , (see notes for keto, and other, options)
- 6 tablespoons boiling water
- 1/4 cup cocoa powder
- Optional: 1 teaspoon vanilla extract
- Optional: large pinch of salt
- 2/3 cup flaxseed meal
- 2 tablespoons miniature chocolate chips, see notes for keto
Instructions
- Preheat the oven to 325°F (160°C). Grease or spray the cups of a 12-cup muffin pan with nonstick cooking spray.
- In a a medium bowl, combine the nut butter, coconut sugar, boiling water, cocoa powder and optional vanilla and salt until blended and glossy.
- Stir in the flaxseed meal (the mixture should be thick, but if it is especially stiff, add a little bit more water).
- Either stir in chocolate chips, or wait, and sprinkle on top.
- Evenly divide batter into prepared muffin cups. If second option was chosen above, sprinkle with chocolate chips.
- Bake in preheated oven for 17 to 19 minutes until the surface of the cookies appears dry and the centers feel just firm to the touch.
- Let cool in pan on a wire rack for 10 minutes. Run knife around edges to loosen, then remove and place on rack to cool completely
Notes
- Keto macros per cookie without chocolate chips: [Calories: 77 / fat: 6.2 g/ sat. fat: 0.6 g/ carbohydrates:4.6 g / sugars: 1 g]
- Keto macros per cookie with sugar-free chocolate chips: [Calories: 88 / fat: 6.9 g/ sat. fat: 1.1 g/ carbohydrates:6.1 g / sugars: 1 g]




Hey, I used peanut butter, very easy to make, they taste great, thanks!!
Excellent, Kevin, so glad you like the recipe! ☺️
Why did the ingredients change on the front page? When you click on the recipe it is back to the recipe I make all the time.
Hi Michelle! I am so sorry, but I am not understanding what is happening on your end based on your comment. I have visited the post page and everything appears to be working correctly. Could you clarify what you mean by the “front page”, the ingredients changing (they all look as they should be on my end; please let me know), or what recipe you are referring to when you say you are being directed to the recipe you make all the time. Thanks so muc.
I only had 32 grams of flax seed left so I substituted the rest with cornmeal, because why not? I also used brown sugar instead of coconut, and cognac instead of vanilla. Oh and I broke up 21 grams of a 77% dark chocolate bar in place of chocolate chips. … And instead of forming cookies I just dumped it all into a bread pan as one mass and shook it to even it out. So I’m not really sure if I made *these* cookies, but whatever I made is quite good.
Brilliant, Dylan! And that’s how new recipes are born 🙂 So glad the recipe worked as a good starting point for your cookies 🙂
I made these into smaller cookie by scooping with a mini ice cream scooped onto a sheet. cut the baking time by more than half. Came out great, thank you
How about subbing date sugar? I’ve been trying to find uses!
Made these keto version with half erythritol & half xylitol in place of the coconut sugar, and skipped the chocolate chips. I tried one but haven’t removed the rest from my silicone muffin cups yet. Pretty yummy, must say! Hope I can keep my family away from them since they have plenty of non keto treats to enjoy, and I love how the bitter chocolate covers any hint of the usual fishy taste flaxseeds sometimes have! I used black cocoa powder, added a 1/2 tsp salt and a few shakes of cayenne, and swapped almond extract fir the vanilla, but that’s just how I like my chocolate 😁
Hi,
I dont use regular sugar or coconut as I have various food sensitivities and can only use Male syrup.
How can I make this substitution please?
Thanks
I
can we use maple syrup sub to coconut sugar?
Yes, that will work fine 🙂
Lovely AGAIN! You’d be surprised by how many of your things I make. Vegan, gf, a few ingredients and quick…what more could I possibly want?
so happy to know you are enjoying the recipes! Thanks for making my day 🙂
Thank you for the substitution notes! I think I’ll be making these!
You are so welcome, Alyson!