Reconstructing historical atmospheric oxygen (O) levels at finer temporal resolution is a top priority for exploring the evolution of life on Earth. This goal, however, is challenged by gaps in traditionally employed sediment-hosted geochemical proxy data. Here, we propose an independent strategy-machine learning with global mafic igneous geochemistry big data to explore atmospheric oxygenation over the last 4.0 billion years. We observe an overall two-step rise of atmospheric O similar to the published curves derived from independent sediment-hosted paleo-oxybarometers but with a more detailed fabric of O fluctuations superimposed. These additional, shorter-term fluctuations are also consistent with previous but less well-established suggestions of O variability. We conclude from this agreement that Earth's oxygenated atmosphere may therefore be at least partly a natural consequence of mantle cooling and specifically that evolving mantle melts collectively have helped modulate the balance of early O sources and sinks.