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Almond Flour Cookies with Dark Chocolate Chips & Pecans (GF)

Published: Oct 13, 2022 · Modified: Dec 5, 2025 by Meghan Kerwin · This post may contain affiliate links · Leave a Comment

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These deliciously soft healthier almond flour cookies are a dream, and I mean that. Dark chocolate chips and pecans mixed in, plus some flaky sea salt on top are chef's kiss! They melt in your mouth and leave you with no guilt (although you should not ever feel that anyways - because balance!)

These cookies are naturally gluten free because we use blanched almond flour, which also adds a nutty flavor and texture. When I need something to satisfy my sweet tooth but I'm wanting something a little less guilty and more nutrient dense, I turn to these cookies. They are SO easy to make and come together super quick!

What is my version of healthy?

My version of "healthy" could be different than your version of healthy. Please keep that in mind and be your own judge. I try to follow an 80/20 lifestyle, which basically just means that 80% of the time I am eating mostly nutrient dense whole foods, lots of veggies, and water to fuel my body and also adding activity throughout my day. That other 20% I leave open for fun things and whatever I'm feeling including rest, self-care, indulgent treats, or special events. I do not follow a diet, rather it is my lifestyle.

In order to maintain this balanced approach, I realize that balance for me means also allowing myself to indulge when needed (ladies, when it's that time of the month - you know what I mean). I do not believe in making myself feel bad about having a treat when I want one and that is why I make healthier alternatives to traditional desserts as well, because despite what some may say - there's always room for dessert!

Be sure to check out some of my other healthier recipes as well!

bite into cookie

What makes these almond flour cookies healthier?

With that being said, my healthier alternatives in my dessert recipes typically include ingredient swaps such as more nutritional flours, refined sugar alternatives, and dairy alternatives. In this recipe we use blanched almond flour which is nutritious but also naturally gluten free. Also swapping regular sugars out for coconut sugar not only adds a delicious sweet flavor but it is unrefined and has a slightly lower glycemic index.

I choose to use dark chocolate chips or chopped dark chocolate bars in this recipe because dark chocolate can actually be good for you, high in antioxidants and minerals such as magnesium. I also add in pecans because not only are they delicious, but they are nutrient dense with fiber and important minerals.

A Note About Chocolate: Most chocolate bars and chocolate chips have sugar added in them, but you can find chocolate that only have unrefined sugars like dates or coconut sugar, such as Hu Chocolate Bars and Chocolate Chips. If you want these cookies to be completely refined sugar free, be sure to read the labels on the chocolate bars or chips and choose accordingly.

Jump to:
  • What is my version of healthy?
  • What makes these almond flour cookies healthier?
  • Ingredients for Almond Flour Cookies
  • How to Make Almond Flour Cookies
  • Variations for Almond Flour Cookies
  • How to Store Almond Flour Cookies
  • Top Tip
  • Almond Flour Dark Chocolate Chip Pecan Cookies (gluten-free and refined sugar free)

Ingredients for Almond Flour Cookies

These almond flour dark chocolate chip pecan cookies are made with simple ingredients. These ingredients are great to keep on hand when you want to make more nutritious swaps in your dessert recipes!

  • Blanched Almond Flour
  • Coconut Sugar - I love Anthony's brand of coconut sugar (and not just because it's my husband's name!)
  • Unsalted Butter
  • Egg
  • Chopped Pecans or any nuts you prefer
  • Dark Chocolate Chips - be sure to use refined sugar free chocolate chips (like these ones made with dates) if you are avoiding refined sugar.
  • Vanilla Extract
  • Pink Himalayan Salt
  • Flaky Sea Salt

How to Make Almond Flour Cookies

Almond flour dark chocolate chip pecan cookies are SO simple to make.

First cream together room temperature butter, sugar, and vanilla until fluffy and thoroughly combined. Then, beat in the egg. Finally, add in all of the dry ingredients including the mix ins - chocolate chips and pecans, and fold together until combined and a cookie dough forms.

Place almond flour cookie dough into the refrigerator to chill for at least 30 minutes, longer if you can. Once chilled, preheat the oven and prepare two baking sheets with parchment paper. Scoop cookie dough onto the trays and round them by rolling them in your hands. Bake and enjoy! It's THAT simple!

Variations for Almond Flour Cookies

  • Dairy Free - Use a dairy free butter or solid coconut oil (keep in mind this will change the flavor).
  • Chocolate Chips - use any kind you like. Dark chocolate whether in a bar form or dark chocolate add the most nutrients. See highlighted note above regarding chocolate and be sure to choose an unrefined sugar chocolate bar to cut up and add in if you are wanting to remain refined sugar free. Most chocolate bars will have added sugar, so be sure to read the labels!
  • Mix Ins - add different kinds of nuts if you don't like pecans or any additional mix ins as desired!

How to Store Almond Flour Cookies

Store baked cookies in an airtight container at room temperature for 2-3 days or up to a week in the refrigerator (if they last that long!)

almond flour cookies

Top Tip

Be sure to chill the completed cookie dough for 30 minutes before baking to ensure the ingredients absorb well and the flavor develops!

If you enjoyed these cookies, be sure to check out my other healthier recipes.

If you made this recipe, BE SURE TO tag me on Instagram @bakingguilty AND please leave a comment OR star rating below! We so greatly appreciate it and hope you love this recipe!

almond flour cookies

Almond Flour Dark Chocolate Chip Pecan Cookies (gluten-free and refined sugar free)

Meghan Kerwin
These soft easy cookies are absolutely delicious and addicting! They are also a healthier alternative to traditional cookies, being gluten free and refined sugar free - YES!
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Prep Time 40 minutes mins
Cook Time 10 minutes mins
Course Dessert
Servings 12 cookies

Ingredients
  

  • ½ cup unsalted butter (1 stick) (room temp.)
  • ¾ cup organic coconut palm sugar
  • 1 large egg
  • 2 cups blanched almond flour
  • ½ teaspoon pink himalayan salt
  • 1 teaspoon vanilla extract
  • 1 cup dark chocolate chips
  • ½ cup chopped pecans (optional)
  • flaky sea salt for topping fresh out of the oven (optional)

Instructions
 

  • In a stand mixer or with an electric hand mixer, cream together the room temperature butter, vanilla extract, and coconut sugar. Once combined, add in egg and mix for two minutes until mixture is fully combined.
  • Fold in almond flour, salt, chocolate chips, and chopped pecans. Once cookie dough forms, cover bowl in plastic wrap and chill in the refrigerator for 30 minutes.
  • Once dough is chilled and ready to be scooped. Preheat oven to 350 degrees Fahrenheit and line two baking sheets with parchment paper.
  • Scoop tablespoon and a half sized cookies out and roll into a ball, then place on cookie tray at least 2 inches apart. Place extra chocolate or pecans on top if desired. Bake for 9 - 12 minutes until baked through but not overbaked. Let cool for a few minutes before diving in. Cookies will be soft and fragile while hot but will be easy to handle when cooled. Enjoy!
Keyword almond flour, chocolate chunk, cookies, gluten free, gluten free cookies, healthy, healthy alternatives, pecan, refined sugar free
Tried this recipe?Let us know how it was!

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Hi, I'm Meg! Founder of Baking Guilty, birthday cake trustee, homebody, and proudly known as the girl who always brings dessert!

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