Methane (CH₄–C) fluxes measured from automated static closed chambers in maize and potato plots in Uasin Gishu County, Kenya. Fluxes were recorded at sub-daily resolution using a cavity ring-down spectrometer (Picarro G2308, Picarro Inc., USA) coupled to 12 automated chambers (50 × 50 × 15 cm), with CH₄ measured simultaneously alongside N₂O and CO₂ during 45-minute sequential closure cycles. Data span from March 2024 to March 2025 at the University of Eldoret, Uasin Gishu County, Kenya (0°34′45″N, 35°18′22″E; 2,213 m a.s.l.) on Ferralsol soils. Four nitrogen fertilisation rates were applied to maize and potato in a randomised complete block design with three replicates: maize at 50 kg N ha⁻¹ , maize at 100 kg N ha⁻¹, potato at 50 kg N ha⁻¹ , and potato at 100 kg N ha⁻¹. Data were collected to characterise CH₄ exchange dynamics – including potential methanotrophy (net CH₄ uptake) in well-drained Ferralsol soils under contrasting crop and fertilisation treatments, and to provide a complete greenhouse gas budget alongside N₂O and CO₂ fluxes. Fluxes are reported in mg CH₄–C m⁻² h⁻¹. Positive values indicate net CH₄ emission; negative values indicate net uptake. This dataset is part of a multi-variable collection archived at PANGAEA.