Line an 8x4-inch or 9x5-inch loaf pan with parchment paper.
In a medium bowl, combine the peanut butter, honey, coconut oil, and vanilla. Add the ground flaxseed and collagen peptides. Stir to combine with a spoon until the mixture is too stiff to stir. Knead into a dough with your hands. Press into the bottom of the prepared pan.
Melt the chocolate in a small pan set over very low heat. Stir constantly until smooth. Pour over the peanut butter layer and tilt the pan to spread it out or spread it with the back of a spoon.
Refrigerate for at least 1 hour before slicing into bars. These bars are best stored in the refrigerator or freezer.