Nitrogen (N) nutrition is a key factor for vegetable growth and yield. However, different rates of nitrogen fertilization may trigger different responses to vegetables. A survey was conducted to investigate the effect of soil fertility management practices on nitrate concentration in vegetables. The survey results were used to plan experiments on the effect of chicken and cattle manures on nitrate levels in Chinese cabbage (Brassica rapa) and amaranthus (Amaranthus cruentus) grown in Tanzania and the patterns of mineral nitrogen in soils under open field conditions. Chicken or cattle manure at 200, 300 kg N ha−1 and 170 250 kg N ha−1 for Chinese cabbage and amaranthus respectively, and control were compared in a randomized complete block design. We observed a higher nitrate content in fertilized Chinese cabbage at day 30 than at day 44 after sowing, ranging from 3243 to 4993 mg kg−1 fresh matter regardless of the N source and rates. Only application of manures at high levels (250 kg N ha−1) induced significantly (p < 0.05) higher nitrate contents in amaranthus at day 28 after sowing, although there was a clear indication of nitrate accumulation even at 170 kg N ha−1 application. Soil NH4+-N + NO3−-N in both Chinese cabbage and amaranthus plots were increased with increasing N application rates and differences between control and amended soils were significant (p < 0.01). There was a positive relationship between NO3− concentration in vegetables and NO3−-N in the rooted top soil layer (0–15 cm). However, higher NH4+ concentrations depressed NO3− build up in crops and a significant negative relationship between soil (NH4+-N)/(NO3−-N) ratio and crop NO3− content was found. It is concluded that low manure application rates result in similar yields to high rates but reduces nitrate accumulation in vegetables and excess mineral nitrogen in soils.