Onboard observer programs have been implemented since the 2000’s to monitor the impact of tropical tuna fisheries on pelagic ecosystems. The recent development of Electronic Monitoring Systems (EMS) offer new insights to improve the monitoring and estimation of discards at sea, which remains a challenge for observers on board purse seiners where catch handling occurs simultaneously at different places on the vessel and often represents large volumes discarded within a short amount of time. In this study, data collected through EMS installed on board French tropical tuna purse seiners operating in the Indian Ocean were used to examine the sorting process and test optimized observer sampling strategies to obtain robust estimates of discards. We used EMS “counts per minute” data to estimate the total amount of discards in numbers, as well as discards per taxa by fishing set. Results indicate differences in the flow of discards among species and sorting location with 82% of the individuals released through the discard belt in the lower deck, the rest being directly released from the upper deck. Observer sampling strategies were simulated with the aim of optimizing the total sampling duration and the duration of sampling sequences by assessing the bias and coefficient of variation of the estimates. Based on these results we recommend a protocol for onboard observers using a minimal coverage of 22 minutes of sorting operations in the lower deck, with sampling sequences of 2 to 4 minutes for large volumes of catch. Further strategies to improve the estimation of discards combining onboard and electronic observations are also discussed.