Line a 8x8-inch baking pan with parchment paper and set aside.
In a large bowl, combine the almond flour, protein powder, natural peanut butter, honey, almond milk, and vanilla extract with a spatula until a thick, uniform dough forms.
Fold the chocolate chips into the mixture, reserving a small handful if you want to sprinkle some on top.
Transfer the mixture to the prepared pan and press firmly and evenly with a spatula to flatten; sprinkle reserved chocolate chips on top if desired.
Refrigerate for 30–60 minutes until set, or freeze for about 25 minutes for a firmer texture.
Lift the set mixture from the pan using the parchment paper and slice into 16 squares.
Store bars in an airtight container in the refrigerator.