Skeletobionts, organisms that attach to or bore into the skeleton of a host, provide a useful system to observe biological interactions over geological timescales. We examined skeletobionts on brachiopod hosts from a stratigraphic section in western New York State that spanned the Lower Kellwasser and Upper Kellwasser events, the two pulses of the Frasnian–Famennian (Late Devonian) mass extinction. The fossils are largely preserved as molds, and even endoskeletobiont borings are often visible with minimal preparation. At least seven major groups of skeletobiont are present including microconchids, stenolaemate and ctenostome bryozoans, hederelloids, and various borings attributed to sponges. The total frequency of skeletobiosis declined significantly across the first extinction pulse (Lower Kellwasser Event), and relative abundance patterns shifted, although the biotic and/or abiotic drivers of these changes require further study. Multivariable logistic regression indicates that large host body size was a strong and consistent predictor of skeletobiosis. Endoskeletobionts were more common in coarser lithologies, reflecting either an ecological preference for sands over muds or a bias against preservation in mudstones. Endoskeletobionts were also more common on ribbed/costate host shells.