The taphonomy and palaeoecology of the early Miocene (Burdigalian) vertebrate assemblage of Ullujaya (East Pisco Basin, Peru) is here described. Vertebrate remains are concentrated in marine facies (Ct1a association) of the exposed Chilcatay Formation (dated 19–18 Ma) deposited within a 30–40 m deep, semi-enclosed, offshore environment. Coupled with ichnological observations, the size distribution of pyrite framboid relics reveals fluctuation of euxinic and oxic-dysoxic conditions at the seafloor. The assemblage is dominated by toothed cetaceans (kentriodontids, squalodelphinids, physeteroids, and the eurhinodelphinid-like Chilcacetus), together with a large dermochelyid turtle, some bony fish, and diverse elasmobranchs, mostly juveniles of Carcharhinus brachyurus and Cosmopolitodus hastalis. The vertebrate assemblage comprises a coastal community, dominated by mesopredators, representative of a warm-temperate, sheltered embayment connected with riverine and open-ocean environments. Vertebrate skeletons are typically disarticulated and incomplete, and some bone elements display shark bite marks. Microborings are observed at the bone surface. Bones exhibit a good degree of apatite mineralisation and bone cavities are locally filled by Ca-Mg carbonates. Our taphonomic observations suggest prolonged flotation of carcasses during which they were subject to biogenic and physical processes of partial destruction (including scavenging by sharks), before final deposition on a soft compact substrate. Preservation was favoured by the oxygen-deficient bottom conditions that inhibited the action of benthic macro-scavengers.