Preheat oven to 375°F and line a baking sheet with parchment paper.
In an electric mixer, combine softened butter, coconut sugar, and cane sugar. Mix on medium to high speed for at least 60 seconds until fluffy, scraping down the sides as needed.
Add egg yolk, vanilla extract, instant coffee, and peanut butter. Whisk again until pale and fluffy, about 60 seconds.
Incorporate almond flour, baking soda, and tapioca flour. Mix for 20-30 seconds until well combined. Fold in chocolate chips.
Using a 1/2 cup measuring cup, scoop dough and roll into balls. Place on the baking sheet and top with additional chocolate chips if desired.
Bake for 10-12 minutes until edges are golden brown and tops are slightly firm. Sprinkle with flaky sea salt if desired, then let cool for 5 minutes before enjoying!