Mediterranean environments are biodiversity hotspots in which strongly seasonal winter rainfall regimes and fire play major roles in driving ecosystem dynamics. Global predictions forecast unreliability of winter rainfall and increases in summer rainfall that are expected to result in major changes in community structure. Mediterranean systems are difficult to model, and although ecophysiological responses can be studied at observational timescales, a long-term understanding is necessary to address uncertainties and refine predictive models at landscape scales. Here we provide a ∼ 1100 year-long palaeoecological reconstruction of vegetation (palynology), fire (sedimentary charcoal) and sedimentological change at a site adjacent to a multi-annual rainfall manipulation experiment designed to test plant population and community responses to altered seasonal regimes in the Greater Cape Floristic Region hotspot (southwestern Africa). We use these data to test whether long-term vegetation dynamics are controlled by changes in rainfall seasonality. We conclude that vegetation dynamics correlate with centennial-scale seasonality fluctuations, with transitions between two ecologically distinct fine-leaved shrub communities. These transitions are consistent with results of responses to experimental manipulations of summer rainfall. This study demonstrates the value of ecophysiological research in interpreting palaeoecological reconstructions and scaling up the results of observational research to answer long-term questions about environmental change. •Projections for Mediterranean areas forecast unreliable winter rainfall.•A 1100 year-long sequence informs of palaeoecological change in the Cape Region.•Vegetation dynamics correlate with centennial seasonality fluctuations.•Landscape dynamics can be predicted from responses at observational timescales.