This article is available at www.sciencedomain.orgAn experiment was carried out in Busia County, Kenya at Emalomba (N 00°25′28.8″ E 034°15′ 51.9″), Nambale District to assess the effects of nitrogen fertilizer rates and legume management options on nitrate nitrogen (NO3-N) under intercropping system. Six soybean residue management options were considered: Sole sorghum, sorghum + soybean left to maturity, sorghum + soybean mulched, sorghum + soybean incorporated, sorghum + soybean exsitu and sorghum + soybean exsitu and plot tilled. Three levels of nitrogen (0kg N ha-1, 40kg N ha-1, and 80kg N ha-1 as urea were applied as top-dress and treatments arranged in randomized complete block design. Soil NO3-N was significantly high (P<0.0010) in topsoil with a notable leaching to subsoil due to precipitation. Control treatments had low soil NO3-N in comparison to other treatments implying that, use of inorganic fertilizers to supplement soil N is important. Fertilizer application at 40kg N ha- 1 with respect to on-farm soybean residue management was in relation to NO3-N supply was in the order: sorghum + soybean left to maturity > sorghum + soybean mulched = sorghum + soybean incorporated. Experimental plots with legume residues removed had significantly (P<0.001) low NO3-N. High leaf NO3-N observed points to transfer of N to sorghum by nitrogen fixation signifying importance of intercropping. There was no significant difference between nitrogen fertilizers applied at 40kg N ha-1 and 80kg N ha-1 irrespective of field managed legume residues. Sorghum intercropped with soybean left to maturity with nitrogen fertilizer applied at 40 kg N ha-1 reflected high (P< 0.001) soil NO3-N in comparison to the other management options. It is therefore recommended as a possible optimum rate and legume residue management option to improve soil NO3-N among small scale households with stretched socio-economic ability in Busia County.