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Background. Despite their immense benefits to smallholder farmers, the complementary effects of combined fertilizer sources with integration of legumes on soil moisture, soil organic carbon content, carbon stocks and their long-term projections in maize systems of Kabete sub-County, Kenya has not been fully investigated. This study will thus develop and promote a site specific technological package that will enhance maize productivity, resilience and sustainability of the smallholder farming systems. Objective. To determine the complementary effects of legume integration and fertilizer application on soil moisture and soil carbon stocks, and carbon stock changes over a 20-year period in maize systems of Kabete sub-County, Kenya. Methodology. The experiment was conducted at Upper Kabete field Research Station of the University of Nairobi during the long (LRS) and short (SRS) rainy seasons of 2015/2016. The experimental design was a Randomized Complete Block Design with a split plot arrangement. The main plots were integration of dolichos into maize (Zea mays L.) systems; (i) as an intercrop (dolichos - Lablab purpureus (L.)/maize) and (ii) in rotation (dolichos-maize), and (iii) sole maize (without dolichos integration). The sub plots were organic and inorganic fertilizers: (i) Farmyard Manure (FYM), (ii) Triple Superphosphate (TSP)+Urea, (iii) FYM+TSP+Urea and (iv) no fertilizer input (control). Soil samples were collected at the end of each cropping season from 0-20 cm depth for determination of; soil moisture (%), soil organic carbon (SOC) content (%), and SOC stocks (t C ha-1). The Rothamsted Carbon model (Roth-C) was used to estimate carbon stock changes over a 20-year period with 1990 as the base year. Results. Significantly (P ≤ 0.05) high levels of soil moisture (31 and 30.1%) and SOC (2.6 and 2.5%) were respectively obtained in maize/dolichos intercrop with application of FYM and FYM+TSP+Urea during the SRS. The same trend in soil moisture and SOC was observed in the LRS. Significantly (P ≤ 0.05) high SOC stocks (t C ha-1) were obtained in maize/dolichos intercrop with FYM (56.20 and 54.71) and TSP+FYM+Urea (54.84 and 52.91) application in the SRS and LRS, respectively. Over a 20-year period, SOC stocks maintained a significant and steady increase and were higher in maize/dolichos intercrop with FYM and FYM+TSP+urea application. The same pattern was noted in dolichos-maize rotation and sole maize systems. Implications. Given the importance of SOC in the improvement of soil quality, incorporation of legumes into maize systems with application of FYM is thus a plausible technological package that could enhance soil fertility and consequently food and nutritional security among smallholder farmers, not only of Kabete sub-County but Kenya and other countries. Conclusion. Significant increases in soil moisture content, organic carbon and, carbon stocks and their projections over a 20-year period were evident in maize/dolichos intercrop with FYM and TSP+FYM+Urea application in both seasons.