Bone histology has proved to be a valuable tool to obtain information about the palaeobiology and early taphonomic history of fossil vertebrates. However, there are still many extinct taxa for which bone histology studies could be applied to deduce information about their life history and early diagenetic changes. Here, we partially fill this gap by studying bone microstructure and bone micropreservation in the third metapodia of Hipparion and Equus recovered from several Miocene, Pliocene, and Pleistocene localities in Turkey. Our histological analysis reveals that most of the bone cortices under study are composed of a well-vascularized fibrolamellar bone. Furthermore, we record the presence of compact coarse cancellous bone in a Hipparion metatarsal. In terms of histological preservation, our findings provide supporting evidence that differences in moisture, oxygen, and/or temperature during fossilisation at the different localities impacted the quality of bone preservation. Bacterial bioerosion was extensive in the samples, and we also identified a specific tunnelling morphology that we tentatively consider to be damage caused by freshwater algae. The present study provides novel insight into the palaeobiology and early diagenetic history of extinct horses from Turkey and sets the stage for further research in this area.