Abstract Metrics of the spatiotemporal variability of the physical and biological properties of Large Marine Ecosystems (LMEs) are critical indices of the trends and changes in these coastal systems. Given that the world's oceans, including coastal systems, are undergoing substantial changes as reported by a range of global assessments, the variability of these changes in space and time is important to understand, if the impacts are to be mitigated and adaptation measures required are to be appropriately applied. We have assessed the trends in Sea Surface Temperature (SST) (1982–2019) and chlorophyll-a concentrations (1997–2019) for all seven of the African LMEs. Our analysis revealed that as a whole almost 99% of all the combined area of African LMEs has warmed. We found rates of SST warming of between 0.11 °C/dec (Agulhas LME) and 0.39 °C/dec (Mediterranean Sea LME) on average for entire LMEs, and regions with rates of as high as 0.58 °C/dec in the Canary Current LME. We also found that 1.1% of the area of the LMEs had cooling trends in association with upwelling regions found in four of the seven LMEs. In this study, we have carefully considered the spatial distribution of warming and cooling in the respective LMEs and identified warming ‘hotspots’ and re-catgorized the LMEs sub-regions into ‘slow’, ‘moderate’, ‘fast’ and ‘superfast’ warming areas, as defined in the Transboundary Waters Assessment Project of the IOC-UNECO-UNEP (2016). In terms of chlorophyll-a, we report that concentration estimates are highly heterogeneous in space and time and that robust trends are, however, difficult to extract from available data. Nevertheless, we do report an overall range in chlorophyll-a concentrations of 0.06–10.9 mg/m3 and the highest median concentrations in the two Eastern Boundary Upwelling Systems, that is, the Benguela Current LME and the Canary Current LME (which also contain the regions with the highest estimates of Net Primary Production (NPP) of 7063 and 7070 mg C/m2/day, respectively). The lowest concentrations are in the oligotrophic Agulhas Current LME, which also has the lowest estimate of NPP of 342 mg C/m2/day. General declines in chlorophyll-a concentrations are observed with statistically significant rates apparent in the Agulhas LME and contrasting areas of local and patchy increases in chlorophyll-a concentrations over time. Decadal trends in NPP are assessed as generally negative in the eastern LMEs and positive in the Western LMEs. The main conclusion from this study is that while the trends themselves are a further iteration of the manifestation of climate change impacts on African LMEs, it is the high degree of heterogeneity in these properties within the LMEs, along the trans-LME distribution in some instances, that must be taken into consideration for assessment of ecosystem impacts and effective management responses.