Paleontological remains retrieved from permafrost represent the most informative records of Pleistocene ecosystems. Different levels of past microbial activity affecting fossil material preservation are presented for two selected bone samples—an almost intact Bison sp. metacarpus (45.0 ± 5.0 14C ka BP) and a weathered Equus sp. metacarpus (37.8 ± 1.7 14C ka BP) from the recently exposed cryogenic geo-contexts in the Yana River basin, NE Yakutia. Diagenetic changes in bone porosity and chemical composition as a result of the past microbial activity were investigated by multiple analytical methods. In the bison bone, which was permafrost-sealed shortly after death of the animal and conserved for ca. 45 ka in a frozen state in a cryolithic formation, only superficial microbial degradation processes were detected. Progressive microbial attacks characterize the horse bone, which was exposed to MIS 3 sub-aerial biogenic decay and modern surficial weathering. This is evidenced by extensive bacterial micro-boring with the typical focal destructions, an increase in microbial porosity, and de-mineralized osseous zones due to waterlogged and poorly oxygenated past depositional conditions. New information contributes to better understanding of the diagenesis particularities and the associated chemical and biological agents of the fossil osteological assemblages with respect to their taphonomic and paleoenvironmental implications.