Abstract Background Evidence suggests that manipulating intercropping timing and stand density within intercropping systems could enhance crop yields. However, our current understanding of the effects of intercropping a cover crop on soil chemical properties and moisture still needs to be improved. This study investigates the effects of intercropping sunn hemp with maize at different timings and stand densities on selected soil properties and crop yield. Materials and methods A split-plot experiment was conducted under the in-field rainwater harvesting (IRWH) tillage. The trial had three intercropping times (simultaneously with maize planting, at V15 maize growth stage, and R1 maize growth stage) as the main plot factors and three stand densities (16, 32, and 48 plants m−2) as the subplot factors, with three replicates for both the 2019/20 and 2020/21 seasons. Changes in soil properties were assessed within the uppermost layer (0-30 cm). Soil moisture content was continuously monitored throughout the growing season and specific soil chemical properties were analyzed at harvest. Results The results showed that the interaction of sunn hemp intercropping period and stand densities did not significantly influence most of the measured soil properties. The early planting of sunn hemp had significantly 32.4% higher soil organic matter (SOM) than the last planting date at low stand density. After two growing seasons SOM, nitrogen, potassium, and manganese were significantly enhanced by 39.7%, 19.0%, 21% and 60.6% respectively. However, during the same period calcium, sodium and iron were significantly reduced by 13.4%, 46.1% and 78.0% respectively. The management of sunn hemp crop had significant effect on maize grain yield across the two seasons. The maize yields in the medium and high stand densities in the first season were significantly 15.3% and 34.3% higher than in the second season, respectively. Conclusion Due to the intercropping treatments, the retention of sunn hemp residues with varying quantities and qualities may have influenced the soil nutrient dynamics in the short-term. Significant changes in soil chemical properties and yield may need more time, and future research should be conducted out in agricultural regions with different soil mineral matrices.