We present a multi-variable field dataset of nitrogen cycling and greenhouse gas measurements from smallholder maize and potato systems in Uasin Gishu County, Kenya (0°34′45″N, 35°18′22″E; 2,213 m a.s.l.), collected from March 2024 to March 2025. The dataset includes (1) automated chamber-based N₂O, CH₄, and CO₂ fluxes measured continously using a cavity ring-down spectrometer (Butterbach-Bahl et al., 1997; Zhu et al., 2024); (2) N₂O isotopologue signatures (δ¹⁵N_bulk, δ¹⁵N_site preference, δ¹⁸O); (3) soil stable isotopes (δ¹³C, δ¹⁵N) and elemental composition; (4) soil mineral nitrogen concentrations (NH₄⁺–N, NO₃⁻–N) from soil cores to 60 cm depth; and (5) continuous soil microclimate and meteorological variables recorded at 15-minute resolution. The dataset spans a full annual cycle, including long rains, dry season, short rains, and fallow periods, with temporal resolution ranging from sub-hourly to monthly. Measurements were conducted on Ferralsol soils (FAO, 2006) within a randomized complete block design with nitrogen fertilisation treatments (0, 50, and 100 kg N ha⁻¹) applied to maize and potato systems. The data were collected to support analysis of nitrogen cycling processes and greenhouse gas emissions in tropical agroecosystems and are suitable for applications in greenhouse gas inventories, process-based modelling, and evaluation of nitrogen management strategies in sub-Saharan Africa.