The early Paleogene is characterized by a “hothouse” environment with repetitive transient warming events known as “hyperthermals.” While these paleoenvironmental changes are well-documented in the Pacific and Atlantic Oceans, records of such changes in the Indian Ocean are limited. Here, we present a new dataset of bulk chemical composition and stable isotopic ratios of the late Paleocene–middle Eocene sediments on the Exmouth Plateau in the mid-latitude eastern Indian Ocean. The bulk δ13C and δ18O suggest a warming period called the Early Eocene Climate Optimum (EECO) and cooling towards the middle Eocene in a long-term perspective. From a short-term perspective, we identified at least five hyperthermals (PETM, H2, I1, J, and ETM3) in the studied sections. We identified six independent components (ICs) corresponding to sediment source materials and post-depositional processes by applying independent component analyses (ICA) to the bulk chemical composition data. The time-series behavior of IC3 indicates an increase in detrital material or a decrease in carbonate rain flux during both long-term (EECO) and short-term (hyperthermal) warming. Additionally, the rise in IC2 implies an increased population of high consumers in the oceanic ecosystem during warming events around the Exmouth Plateau. Other ICs (IC1, IC4, IC5, and IC6), indicators of diagenetic processes and post-depositional remobilization of elements, showed excursions across hyperthermal horizons. These observations indicate that changes in the redox state of pore or bottom water in the Exmouth Plateau are associated with hyperthermals.