Heat the oven to 350°F (177°C). Line a baking sheet with parchment paper or a silicone mat and set aside.
In a large bowl, whisk the eggs until lightly frothy. Add the peanut butter, Greek yogurt and vanilla; beat with a whisk or electric hand mixer on low until smooth and well combined.
In a separate bowl combine the oats, protein powder, coconut sugar, baking powder, baking soda, cinnamon, nutmeg, and sea salt. Stir the dry mix so there are no lumps.
Fold the dry ingredients into the wet mixture with a sturdy spatula until a sticky dough forms. Fold in the chocolate chips until evenly distributed.
Scoop rounded tablespoons of dough onto the prepared sheet — you should get about 12 cookies. Press each mound lightly with the back of a spoon to flatten them to roughly 1/2-inch thickness; press a couple extra chips on top for presentation.
Chill the cookie sheet in the fridge for 15–20 minutes. This resting step makes the cookies spread less and keeps them thick and tender after baking.
Bake on the center rack for 10–13 minutes, until the edges are set and the tops look matte but not dry. Rotate the pan halfway through if your oven has hot spots.
Let the cookies cool on the baking sheet for 8–10 minutes, then transfer to a wire rack to finish cooling. They firm up as they cool but remain soft in the center.
Store cooled cookies in an airtight container at room temperature for up to 3 days, or refrigerate for up to a week.