Morphological changes in the skeletons of working animals such as reindeer, horse, and cattle have long been observed and documented in the archaeological record. Activities such as riding, carrying cargo on their backs, and pulling vehicles like sleds and ploughs throughout an animal’s life history cause alterations and variations to skeletal tissue. Such alterations include paleopathological lesions, entheseal changes (EC)—alterations in muscle, tendon, and ligament attachment sites on bone—and variations in cross-sectional bone geometry (CSBG). These clues are helpful for reconstructing human-animal relationships in faunal remains of our archaeological past. However, other factors influence the morphological appearance of skeletal tissue besides working activities, such as age, sex, body size, nutrition, genetics, environmental factors, and management by human caretakers. This article explores how paleopathological lesions, EC, and CSBG in faunal skeletal remains are examined to reconstruct working activity and changes to human-animal relationships in the archaeological record. In particular, we discuss two primary topics of inquiry: (1) a review of paleopathological identifiers in working animals such as cattle, horse, camel, and reindeer; and (2) how EC and CSBG are understood in terms of bone functional adaptation, and their application in working and non-working animals such as reindeer and horse. Next, we analyze each topic highlighting their benefits and limitations, including how they contribute to archeological understandings of human-animal relationships in the past, as well as their implications for future research.