This dataset contains the size measurements of both whole and fragmented planktonic foraminifera recovered from 83 sediment core-top samples in the tropical Indian Ocean. These core-top samples were collected during different cruises (1996 RV Marion Dufresne MOZAPHARE expedition and the BARAT 94 cruise onboard the RV Baruna Jaya I) and were archived in the repositories at the Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement (CEREGE, France) and Laboratoire des Sciences du Climat et de l'Environnement (LSCE, France). The spatial coverage of the samples includes the Mozambique Channel, Bay of Bengal, Offshore Java, Central Indian Ocean, and Arabian Sea. The water depths of the coretops range between 364 m and 4425 m. The morphometry of the planktonic foraminifera species was acquired by a state-of-the-art automated machine (MiSo) and the classification of the species was based on a Convolutional Neural Network model. Also included in this dataset are some physico-chemical surface and bottom water environmental parameters at the sites compiled from various modern oceanographic datasets to investigate the environmental drivers of planktonic foraminifera size in the tropical Indian Ocean. The dataset includes size-derived parameters and assemblage composition.