The study was carried out at Lichinga and Sussundenga Research Station to assess the effects of cow manure and inorganic fertilizer on height, Stover yield, grain yield, yield quality for both maize and legumes of a maize/legume intercrop. A factorial design experiment with a split plot arrangement and replicated three times per site was used. The treatments comprised two intercropping systems of maize/bean and maize/soybean and five fertilizer application rates: Control, cow manure (5 ton ha -1 ), cow manure 1.25 ton ha -1 + 100 kg NPK ha -1 , cow manure 2.5 ton ha -1 + 50 kg NPK ha -1 and 200 kg NPK ha -1 . Results showed that the Stover weight, plant height, hundred grain weight and grain yields had significantly differences (P ≤ 0.05) when cow manure was combined with NPK fertilizers. Maize grown in Sussundenga gave higher values of Stover weight, plant height, hundred seed weight and total grain yield compared to Lichinga. In fact, higher maize growth parameters were improved by intercropping with common bean than in soybean in both locations, a fact attributed to the better utilization of the available resources by maize/common bean intercrop. Combination of 1.25 ton ha -1 of cow manure and NPK 100 kg ha -1 fertilizers significantly (P ≤ 0.05) increased the yield of maize over application of cow manure or NPK alone and farmers are recommended to adopt this production system in the two sites.