Farmers in Bukoba district, northwest Tanzania, are confronted with continuous decline in crop productivity. Previous studies as well as farmer interviews indicate that soil fertility is the major constraint in the banana based land use systems. Nutrient fluxes in these systems were not well documented. In the study presented here data were collected to calculate nutrient balances for different agro-ecological zones. Emphasis was given to homegarden productivity the role of cattle and quantification of nutrient loss from leaching. Households with different soil fertility management levels were included in the studies. Results showed that nutrient balances were negative in all agro-ecological zones for households without cattle. Major sources of nutrient loss were harvest of crops residues, especially beans, leaching and denitrification. Nutrient balances were less negative in agro-ecological zones with less rainfall and lower population densities. The results from this study emphasize the importance of cattle in maintaining soil fertility, but few households have access to this source. Other sources of nutrient input besides cattle must be considered to involve low resource households in the improvement of their soil nutrient balances. Recommendations made are, amongst others, introduction of slow-release industrial fertilizers and split applications, on-farm coffee de-hulling, introduction of green manures and improvement of small ruminant management.