<p><strong>Background.</strong> 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. <strong>Objective</strong>. 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. <strong>Methodology.</strong> 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 (Z<em>ea mays L.</em>) systems; (i) as an intercrop (dolichos - <em>Lablab purpureus </em>(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<sup>-1</sup>). The Rothamsted Carbon model (Roth-C) was used to estimate carbon stock changes over a 20-year period with 1990 as the base year. <strong>Results.</strong> 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<sup>-1</sup>) 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.<span style="text-decoration: line-through;"> </span>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. <strong>Implications.</strong> 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. <strong>Conclusion.</strong> 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.</p>