Synoptic intensification or relaxation of upwelling favorable winds are major sources of variability in eastern boundary upwelling systems. This study aims to investigate their impact on the planktonic ecosystem of the South Senegalese Upwelling Sector (SSUS), located south of the Cape Verde peninsula over a wide and shallow continental shelf. Numerical experiments using a three-dimensional coupled physical–biogeochemical model with four plankton functional types simulated the response of the coastal planktonic ecosystem to idealized synoptic (∼10 days) wind intensification and relaxation of the same amplitude. We find that these perturbations induce spatio-temporal oscillations of plankton concentrations. Zooplankton response occurred with a time lag that manifests itself in space as an equatorward/downstream shift in distribution relative to phytoplankton. Overall, the transmission of the synoptic perturbation from the physics to zooplankton is characterized by a damping in relative anomalies. All these elements and the weakness of the asymmetries in the biogeochemical/planktonic ecosystem responses between intensification and relaxation events support the hypothesis that synoptic variability has limited impact on the climatological state of low–latitude upwelling systems such as the SSUS. PLAIN LANGUAGE SUMMARY In some coastal regions of the world such as off Senegal, winds preferentially blow alongshore and induce subsurface, cold and nutrient rich waters to rise to the surface layer and favor the development of plankton blooms. These so-called upwelling favorable winds are not steady. Their fluctuations produce dynamical and biogeochemical variability over a broad range of scales. Here, we studied the biogeochemical effect of 10-day (i.e. weather or synoptic) wind fluctuations over the southern Senegal continental shelf. We used a numerical model with a simplified planktonic ecosystem consisting of two phytoplankton and two zooplankton size classes. The wind perturbations modulate ocean physics, the enrichment of the sun-lit surface layer in nutrients and the planktonic ecosystem. The plankton’s response to wind fluctuations exhibited oscillations more complex and relatively less intense than those of the wind. The modest effect of the studied short-term wind fluctuations on plankton found in this study may be specific to low-latitude coastal oceans with wide continental shelves.