The datasets were collected from experimental sites in Tharaka-Nithi County, Kenya, over two consecutive cropping seasons (one year). The study aimed to assess the effects of different soil fertility management strategies on greenhouse gas (GHG) emissions. The treatments investigated included inorganic fertilizer, animal manure, animal manure combined with inorganic fertilizer, and a Control (No external input). The dataset includes GHG fluxes, rainfall distribution, soil moisture content, soil temperature, Mineral Nitrogen, and Leaf Area Index. The GHG data (carbon dioxide [CO₂], methane [CH₄], and nitrous oxide [N₂O]) were measured using static chamber methods, with gas samples analyzed through gas chromatography. Meteorological variables such as rainfall and soil moisture were monitored throughout the study. This dataset is supplementary to the research article by Musafiri, C.M., Macharia, J.M., Kiboi, M.N., Ng'etich, O.K., Shisanya, C.A., Okeyo, J.M., Mugendi, D.N., Okwuosa, E.A. and Ngetich, F.K., 2020. Soil greenhouse gas fluxes from maize cropping system under different soil fertility management technologies in Kenya. Agriculture, Ecosystems & Environment, 301, p.107064. https://doi.org/10.1016/j.agee.2020.107064