N₂O isotopologue signatures – including bulk δ¹⁵N (‰ vs. air N₂), intramolecular site preference (δ¹⁵N^SP = δ¹⁵Nα − δ¹⁵Nβ, ‰), and δ¹⁸O (‰ vs. VSMOW) – measured from headspace gas samples collected monthly from static chambers in smallholder maize and potato plots in Uasin Gishu County, Kenya. This is the first field-scale N₂O isotopologue dataset from a sub-Saharan African agroecosystem. Gas samples were collected by syringe (180 mL per sample) 36 minutes after chamber closure and stored in pre-evacuated crimp-top vials. Isotopologue composition was determined using an Elementar Trace Gas purge-and-trap system coupled to an Elementar IsoPrime100 isotope ratio mass spectrometer (IRMS); five Faraday cups (m/z 30, 31, 44, 45, 46) measured N₂O isotopologues simultaneously. 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.). 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. Samples with IRMS peak area below 5 mV·s are flagged as low-signal and excluded from pathway partitioning calculations. Data were collected to attribute N₂O emissions to specific microbial production pathways and to quantify in-soil N₂O reduction to N₂ across contrasting crop and fertilisation treatments. This dataset is part of a multi-variable collection archived at PANGAEA.