Preheat the oven to 350°F (175°C). Prepare a baking sheet by lining it with parchment paper or a silicone baking mat.
In a medium bowl, stir together the whole wheat pastry flour, baking soda, and sea salt until evenly combined.
In a separate large bowl, whisk the melted coconut oil, Greek yogurt, coconut sugar, vanilla extract, and egg until the mixture looks smooth and well blended.
Gradually add the dry ingredients into the wet ingredients. Stir gently until everything is just combined. Avoid overmixing.
Fold the dark chocolate chips into the dough until evenly distributed.
Scoop heaping tablespoons of dough and place them onto the prepared baking sheet. Slightly flatten each dough ball with the back of a spoon or your fingers to shape into cookies.
Add a few extra chocolate chips on top if desired.
Bake for 9–10 minutes, or until the edges turn lightly golden brown.
Remove from the oven and allow the cookies to rest on the baking sheet for about 10 minutes. They will appear soft at first but will firm up as they cool. Transfer to a wire rack and let them cool completely.