Heat the oven: Preheat to 350°F (175°C). Line a baking sheet with parchment paper.
Mix the wet ingredients: In a large bowl, whisk the eggs, melted butter or coconut oil, maple syrup, and vanilla until smooth and glossy.
Add the dry ingredients: Sprinkle in protein powder, almond flour, oat flour, coconut sugar, baking powder, baking soda, and salt.
Stir with a spatula until a thick dough forms. It should be soft but scoopable, not runny.
Adjust texture if needed: If the dough feels crumbly, add 1–2 tablespoons of milk. If it’s too loose, add 1–2 tablespoons oat flour.
Fold in the chips: Stir in the mini chocolate chips (and nuts, if using) until evenly distributed.
Scoop and shape: Use a 2-tablespoon cookie scoop to portion dough onto the sheet, spacing 2 inches apart.
Lightly press each mound to about 1/2 inch thick; protein cookies don’t spread much.
Bake: Bake 9–12 minutes, until the edges look set and lightly golden. The centers should still look a touch soft.
Rest on the pan: Let cookies cool on the baking sheet for 8–10 minutes to finish setting, then transfer to a rack to cool completely.
Optional finish: While warm, sprinkle with a pinch of flaky salt to sharpen the chocolate flavor.