An intensification of upwelling-favorable winds in recent decades has been detected in some of the main eastern boundary current systems, especially at higher latitudes, but the response of coastal phytoplankton communities in the Humboldt Current System (HCS) remains unknown. At higher latitudes in the HCS (35–40°S), strong seasonality in wind-driven upwelling during spring-summer coincides with an annual increase in coastal chlorophyll-a and primary production, and a dominance of micro-phytoplankton. In order to understand the effects of potential upwelling intensification on the micro-phytoplankton community in this region, annual and inter-annual variability in its structure (total and taxa-specific abundance and biomass) and its association with oceanographic fluctuations were analyzed using in situ time series data (2002–2009) from a shelf station off Concepcion (36.5°S). At the annual scale, total mean abundance and biomass, attributed to a few dominant diatom taxa, were at least one order of magnitude greater during spring-summer than autumn-winter, in association with changes in upwelling and surface salinity and temperature, whereas macro-nutrient concentrations remained relatively high all the year. At the inter-annual scale, total abundance and biomass decreased during the upwelling season of the 2006–2009 period compared with the 2002–2006 period, notably due to lower abundances of Skeletonema and Leptocylindrus, but the relative dominance of a few taxa was maintained. The 2006–2009 period was characterized by higher upwelling intensity, colder and higher salinity waters, and changes in nutrient concentrations and ratios compared with the first period. The inter-annual changes in the micro-phytoplankton community were mostly associated with changes in surface salinity and temperature (changes in upwelling intensity) but also with changes in Si/N and N/P, which relate to other land-derived processes.