Use a hand mixer to cream together softened butter and coconut sugar until smooth. Turn the mixer speed to low and add in egg, egg yolk, and vanilla extract. Mix until well combined.
Fold in baking soda, salt, and almond flour until well combined.
Fold the chocolate chips and chunks into the dough until well combined.
Let the dough chill for 30 minutes.
After the dough has chilled, lined a sheet pan with parchment paper and preheat oven to 350 degrees.
Use a tablespoon cookie dough scoop to scoop the dough and drop onto the parchment lined sheet pan 2 inches apart. You can lightly press in a few more chocolate chips or smaller pieces of chocolate in the top of the cookies if you like.
Bake the cookies at 350 degrees for 8-10 minutes (mine went for exactly 9 minutes). You’ll know they’re ready when the bottom of the cookie is golden, the edges are set, but the middle is still soft and fudgy.
Remove the cookies from the oven and let cool on the sheet pan for 1-2 minutes before transferring them to a wire rack to finish cooling. Top with flaky sea salt, while warm.
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