Sedimentary records of the Early Cenozoic indicate a series of events with climatic and carbon cycle variability known as hyperthermals. A ~350-kyr-long event of environmental disruption during the Paleocene, not described before and here named Selandian-Thanetian Transition Event (STTE), has been recognized and well constrained in the western Tethys Contessa Road section (Gubbio, Italy) through high-resolution biostratigraphic, geochemical, and rock-magnetic data. The STTE exhibits peculiar stressed ecological responses among calcareous nannofossils and foraminifera, which highlight marked environmental perturbation affecting the biosphere. The environmental instability is not confined within the photic zone but extends to the seafloor leading to little more trophic conditions of the sea surface waters with an enhanced, but of short measure, nutrient availability on the seafloor conditions and marked rise of lysocline. Magnetic Susceptibly (MS) is dominantly controlled by the balance between carbonate productivity and detrital supply, as evidenced by the strong correlation between MS and CaCO3 (%) (r2 = −0.72). However, we also document two components in the isothermal remanent magnetization (IRM) and first-order reversal curves (FORC) diagrams that prove the occurrence of biogenic magnetite throughout the STTE. Systematic variations in bio-geochemical and magnetic parameters show the relative abundance of carbonate production (or inversely dissolution of carbonate) versus detrital supply during the STTE, which induced higher populations of magnetotactic bacteria through increased terrigenous input and, therefore, increased nutrient supply. Noteworthy, the uppermost part of the STTE includes the equivalent of the suspected hyperthermal, short-lived Early Late Paleocene Event (ELPE). The ELPE event shows an episode of increase in magnetic properties of the sediments, including an increase in magnetofossil concentration, as indicated by IRM components and FORC diagrams. The comparison of biotic and abiotic records throughout the STTE at Contessa Road section with available data across the ELPE from former investigated ocean and land-based sites provides lines of evidence that this latter event might be indeed only the terminal part of a long-lasting environmental change than hitherto supposed.