Line the 8x8-inch pan with parchment paper so the bars can be lifted out easily.
In a large mixing bowl, combine the almond flour and protein powder; stir to blend evenly.
Add the natural peanut butter, honey, almond milk, and vanilla extract to the dry mixture and stir with a spatula until a uniform, slightly sticky dough forms.
Fold in the chocolate chips, reserving a few to sprinkle on top if desired.
Press the mixture firmly and evenly into the prepared pan using the spatula so the surface is compact.
Refrigerate the pan for 30–60 minutes (or freeze for about 25 minutes) until the bars are set.
Lift the set mixture from the pan using the parchment and cut into 16 squares.
Store the bars in an airtight container in the refrigerator.