The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) time series shows high variability of surface chlorophyll at seasonal and intraseasonal time scales in the oligotrophic southern tropical Indian Ocean thermocline ridge called the Seychelles-Chagos thermocline ridge (SCTR). The SCTR is characterized by an open ocean upwelling due to local Ekman pumping, which annually maintains the mixed layer (ML) shallow and is responsive to atmospheric forcing and in particular to the Madden-Julian Oscillation (MJO) at an intraseasonal time scale. Here we present an overview of SCTR biogeochemistry and investigate the physical processes driving the response observed at seasonal and intraseasonal time scales. Using satellite observations and biophysical ocean simulations, we show that seasonal and intraseasonal SeaWiFS signals (in austral winter and during MJO events, respectively) correspond to wind-induced mixing episodes. During such episodes, entrainment fertilizes the ML and allows phytoplankton production. Increased surface production is compensated by a decrease in the subsurface due to light limitation, leading to no significant change in integrated biomass and carbon export. Satellite observations and model results support the conclusion that the biogeochemical response to MJO is highly dependent on interannual variability of thermocline depth. Following Indian Ocean Dipole events, deepened nutrient-rich waters prevent nutrient input into the ML, decreasing the biogeochemical response to MJO. These results shed light on the physical processes at work in the strong surface temperature response to MJO in this region and suggest that entrainment cooling can play a role in the temperature signature to the MJO but is highly modulated by basin-scale interannual variability.