A negative correlation between body size and the latitudinal temperature gradient is well established for extant terrestrial endotherms but less so in the fossil record. Here we analyze the middle Eocene site of Geiseltal (Germany), whose record is considered to span ca. 5 Myrs of gradual global cooling, and generate one of the most extensive mammalian Paleogene body size datasets outside North America. The δ18O and δ13C isotopic analysis of bioapatite reveals signatures indicative of a humid, subtropical forest with no apparent climatic change across Geiseltal. Yet, body mass of hippomorphs and tapiromorphs diverges rapidly from a respective median body size of 39 kg and 124 kg at the base of the succession to 26 kg and 223 kg at the top. We attribute the divergent body mass evolution to a disparity in lifestyle, in which both taxa maximize their body size-related selective advantages. Our results therefore support the view that intrinsic biotic processes are an important driver of body mass outside of abrupt climate events. Moreover, the taxonomy previously used to infer the duration of the Geiseltal biota is not reproducible, which precludes chronological correlation with Eocene marine temperature curves.