Preheat the oven to 350°F (177°C) and line a baking sheet with parchment paper.
In a mixing bowl, beat the room-temperature butter until smooth. Gradually beat in the maple syrup until light and whipped.
Add the peanut butter and mix until combined, then beat in the egg and vanilla extract until incorporated.
Fold in the almond flour, protein powder, baking soda, and kosher salt until a sticky dough forms.
Stir in the chocolate chips or chunks evenly through the dough.
Scoop rounded 1-tablespoon portions of dough (the dough will be wet) and place them about 2 inches apart on the prepared baking sheet.
Bake for 7 minutes, then remove the pan and gently tap the baking sheet on the counter to deflate each cookie slightly.
Return the cookies to the oven and bake 3–4 more minutes, until edges are lightly browned but centers are still slightly soft.
Remove from the oven and gently tap the baking sheet 1–2 times, then let the cookies cool on the baking sheet. Sprinkle with flaky sea salt if desired.