Abstract While the far Western Tropical Pacific is known for interannual variability, we find intraseasonal variability (ISV) actually dominates surface chlorophyll (SChl) fluctuations, explaining >30% of variance. The Madden‐Julian Oscillation (MJO) acts as the key driver through three mechanisms: (a) positive MJO phase vertical mixing (enhanced winds deepen the mixed layer, entraining subsurface nutrients, most effective east of Papua New Guinea); (b) MJO‐associated precipitation‐driven atmospheric wet nitrogen deposition (regulating SChl in the NEC bifurcation and northern nascent NECC); and (c) negative MJO phase horizontal advection (strengthened currents transport nutrient‐rich waters from the Maluku Channel and northern Papua New Guinea to the nascent NECC). In this global biodiversity hotspot, incorporating these coupled MJO‐driven processes into ecosystem models is essential for improving predictive skill and managing biogeochemical dynamics.