The Benguela Upwelling System (BUS) is among the most productive ecosystems globally, supporting numerous fisheries and ecosystem services in Southern Africa. Sea‐viewing Wide Field‐of‐view Sensor and Moderate‐resolution Imaging Spectroradiometer‐Aqua chlorophyll a (Chla) concentrations between September 1997 and February 2018 were used to investigate long‐term trends in phytoplankton biomass and size structure (microphytoplankton [>20 μm], nanophytoplankton [2–20 μm], and picophytoplankton [<2 μm]) in the Northern Benguela, Southern Benguela (SB), and Agulhas Bank (AB) shelf and open ocean regions of the BUS. Trends in upwelling and correlations with Chla and size structure were examined. Increasing Chla and microphytoplankton trends occurred in the Northern Benguela shelf and open ocean, while decreases were evident on the SB shelf in all seasons. In the SB open ocean, small increases occurred during austral winter, with a decrease in spring. On the AB shelf, increases in Chla and microphytoplankton occurred in summer with decreases during the other seasons. Patterns differed in the AB open ocean, with increases in winter and spring and decreases in summer and autumn. Although R2 values indicated that linear trends accounted for a reasonable portion of the variance, and most trends were statistically significant, they showed only small changes on the shelf domains and little to no change in the open ocean. Strong correlations between upwelling, Chla, and the size classes were observed, but distinct seasonal differences occurred in each region. This is the first 20‐year analysis of phytoplankton biomass and community structure in the BUS and provides a baseline against which future changes can be monitored.