Since 2012, we have investigated a stratigraphic section encompassing the late Eocene–earliest Oligocene interval at Shapaja (Tarapoto area, Peruvian Amazonia, ca. 7°S), through paleontological and geological fieldwork. The measured sedimentary series (120 m-thick [West] plus 90 m-thick [East]), assigned to the upper member of the Pozo Formation, records fluvial micro-conglomeratic lenses intercalated with floodplain and evaporite-rich fine red deposits, estuarine/coastal-plain tidally-influenced fine sandstones, and oxbow lake nodule-rich blue clays. This sedimentary shift coincides locally with the demise of the large Eocene coastal-plain wetland known as Pozo System. The late Eocene–early Oligocene Shapaja section was extensively sampled for chemostratigraphy (δ13C on dispersed organic matter and pedogenic carbonate nodules), which in turn allowed for refining the location of the Eocene-Oligocene Transition (EOT) and other climatic events recognized at a global scale (i.e., Oi-1 and Oi-1a). The section has yielded nine fossil localities with plant remains (leaves, wood, charophytes, and palynomorphs), mollusks, decapods, and/or vertebrates (selachians, actinopterygians, lungfishes, amphibians, sauropsids, and mammals), documenting ~130 distinct taxa. Four localities of the upper member of the Pozo Formation at Shapaja predate the EOT, one is clearly within the EOT, while four are earliest/early Oligocene in age. The small leaf impressions found along the Shapaja section could be indicative of dry and/or seasonal conditions for this region throughout and after the EOT. Monkeys, indicative of tropical rainforest environments, are only recorded in a latest Eocene locality (TAR-21). Two biotic turnovers are perceptible in the selachian, metatherian, and rodent communities, well before the EOT [~35–36 Ma] and a few hundred thousand years after the EOT [~33 Ma]. The latter turnover seems to be primarily related to a global sea-level drop (ichthyofauna: marine-littoral elements replaced by obligate freshwater taxa) and/or the onset of a drier and more seasonal climate in early Oligocene times (terrestrial components). Changes in the structure of the Shapaja paleocommunities were mostly driven by the flexural subsidence during the late Eocene, and then globally driven by the earliest Oligocene climatic deterioration.