This paper examines the factors limiting vegetable crop yields in the uplands of Southeast Asia. A survey of farms and soil sampling conducted in the upper Manupali watershed, Mindinao, the Philippines found large differences in the yields of four common crops: tomato, cabbage, potato, and Chinese cabbage. Nitrogen application was most influential on tomato and cabbage yields; proportion of sand in the top soil and use of fungicide were the primary determinants of potato yields, and family labor availability had the greatest effect on Chinese cabbage yields. Based on multivariate data analysis, the farming systems were grouped into higher and lower external nutrient systems (HEN and LEN). Further application of soil conservation techniques, cropping sequences, and plant protection practices would increase the sustainability of both system types. LEN systems would benefit from increased nutrient application while use of labor saving technologies, crop diversification, and more efficient use of fertilizer would enhance HEN system sustainability.