Abstract The ‘COPSE’ (Carbon, Oxygen, Phosphorus, Sulphur and Evolution) biogeochemical model predicts the coupled histories and controls on atmospheric O2, CO2 and ocean composition over Phanerozoic time. The forwards modelling approach utilized in COPSE makes it a useful tool for testing mechanistic hypotheses against geochemical data and it has been extended and altered a number of times since being published in 2004. Here we undertake a wholesale revision of the model, incorporating: (1) elaboration and updating of the external forcing factors; (2) improved representation of existing processes, including plant effects on weathering and ocean anoxia; (3) inclusion of additional processes and tracers, including seafloor weathering, volcanic rock weathering and 87Sr/86Sr; (4) updating of the present-day baseline fluxes; and (5) a more efficient and robust numerical scheme. A key aim is to explore how sensitive predictions of atmospheric CO2, O2 and ocean composition are to model updates and ongoing uncertainties. The revised model reasonably captures the long-term trends in Phanerozoic geochemical proxies for atmospheric pCO2, pO2, ocean [SO4], carbonate δ13C, sulphate δ34S and carbonate 87Sr/86Sr. It predicts a two-phase drawdown of atmospheric CO2 with the rise of land plants and associated cooling phases in the Late Ordovician and Devonian-early Carboniferous, followed by broad peaks of atmospheric CO2 and temperature in the Triassic and mid-Cretaceous – although some of the structure in the CO2 proxy record is missed. The model robustly predicts a mid-Paleozoic oxygenation event due to the earliest land plants, with O2 rising from ~ 5% to > 17% of the atmosphere and oxygenating the ocean. Thereafter, atmospheric O2 is effectively regulated with remaining fluctuations being a Carboniferous–Permian O2 peak ~ 26% linked to burial of terrestrial organic matter in coal swamps, a Triassic–Jurassic O2 minimum ~ 21% linked to low uplift, a Cretaceous O2 peak ~ 26% linked to high degassing and weathering fluxes, and a Cenozoic O2 decline.