Conservation management strategies have been recommended to enhance soil fertility, moisture retention, crop yield, and yield stability in rainfed agriculture. However, there is limited research on yield stability. We evaluated the effect of integrating soil inputs in conservation tillage on yield and yield stability in Meru South, Upper Eastern Kenya, for eleven consecutive cropping seasons. The trial treatments included conservation tillage without soil inputs (Mt), conservation tillage with soil inputs: sole inorganic fertilizer (F), residue + inorganic fertilizer (RF), residue + inorganic fertilizer + manure (RFM), residue + manure + legume Dolichos Lablab L. (RML), residue + Tithonia + manure (RTM), residue + Tithonia + phosphate rock (RTP) and conventional tillage (Control). Conservation tillage with RFM was the best-fit strategy for enhancing yields. There was heterogeneity in yield residual variance. A larger residual variance implied lesser yield stability. Mt treatment had the least yield residual variance of 0.12 Mg ha−2, followed by Ct and RML, 0.15 Mg ha−2, while RTM had the highest yield residual variance of 0.62 Mg ha−2. Contrarily, the most stable treatments had the least average yields. The study indicated a positive influence of incorporating soil inputs in conservation tillage on yield and suggests longer-term research for yield stability.