Metatheria (Mammalia) were remarkable faunal components of South American Cenozoic history. Now represented solely by the marsupials (e.g., opossums, kangaroos), metatherians evolved multiple adaptive types with greater past diversity and abundance than today. One important chapter of this history is the Eocene–Oligocene transition, a period of considerable changes worldwide, with marked extinctions, diversity changes, and drastic climatic processes (i.e., transition from the early Cenozoic “Greenhouse World” to the post-Eocene “Icehouse World”). For Metatheria, the Eocene-Oligocene transition is considered the major turnover point in their evolutionary history in South America, an assumption mainly based on the fossil record from Argentinian Patagonia. However, the Eocene–Oligocene transition is scarcely known at tropical latitudes of South America, like other time intervals, since this region is still poorly understood from a paleontological and geological standpoint. This study aims at partly filling this knowledge gap, by reporting preliminary identifications of metatherians from the late Eocene–early Oligocene Shapaja section, near Tarapoto, Peruvian Amazonia. Nine fossiliferous localities of the Pozo Formation were dated by chemostratigraphy and explored through wet screening (1–2 mm meshes), which allowed recovering small-sized fossils (plants, mollusks, decapods, fishes, amphibians, reptiles, and many mammals). Metatherians were found in most localities and, according to their taxonomic composition, three assemblages could be recognized throughout the section, a pattern also observed in rodents and fishes. The oldest assemblage (TAR-74, early late Eocene) is composed of only one new prepidolopid polydolopimorphian. The second assemblage (TAR-20, 72, 21), latest Eocene, encompasses scarce and fragmentary remains of another probable prepidolopid, numerous remains of a small gerbil-like argyrolagid, and teeth of palaeothentoids, an extinct clade of paucituberculatans, with two basal forms plus two palaeothentines. These records represent the oldest occurrences of Palaeothentinae and Argyrolagidae, and the northernmost record of the latter clade. The earliest Oligocene localities yielded none (TAR-22) or few fragmented metatherian remains (TAR-13), possibly due to taphonomic biases, being considered transitional. Finally, the third assemblage (TAR-01, early Oligocene) includes one larger, rarer argyrolagid and several palaeothentoids (three basal taxa, three palaeothentids, and one abderitid). Thus, the Shapaja section does not attest to a smaller diversity around the Eocene–Oligocene transition. However, the changes in the taxonomic composition of the assemblages, along with other geological and paleontological data, point to two biotic turnovers. The first one, during the late Eocene, has probably been driven by regional processes related to the Andean orogeny, which led to an episodic marine incursion in this area. The later biotic turnover, by contrast, seems to be related to the Eocene–Oligocene transition global processes, namely the great drop in sea level and the onset of drier and cooler climates worldwide, with decreased precipitation and increased seasonality. Indeed, fossil plants from Shapaja indicate the occurrence of multi-stratified rainforests during the latest Eocene and more open, deciduous forests in the earliest Oligocene. Finally, the Shapaja section highlights the importance of fieldwork and research efforts in northern South America, to get better correlations with middle and high latitudes localities, and thus a refined paleobiodiversity picture in the whole continent