Recent scholars and development workers have emphasized on Developing World farmers’ farming materials and ethno-ecological knowledge and its potential for practical use in the fields. The northeast upland Khasi of Bangladesh what kind and extent of knowledge and farming materials are being used to augment of soil-nutrient to grow the tree crop in uphill is not uncovered. The aim of the present study was to explore their manure concept, source of manure and management system with practice in tree crop farming how their farming knowledge was integrated with indigenous knowledge and modern scientific knowledge. In this study the data was obtained using qualitative approach through participant observation and in-depth interviews from the local participants of the study area. Later elicited data were analyzed and categorized to find out their system. The findings illustrated that the global changing trend and social, political, economic factors as well as individual initiative bounded Khasi to be influenced and perceived the modern farming phenomenon and assimilated diverse origin farming inputs and knowledge systems. To explore these issues and the impact of prevalent farming concepts, the study investigated these factors, which revealed the inherent consequence of Khasi farmers’ soil fertilizing knowledge with tree growth. The result of investigation signified that the Khasi soil-fertilizing procedures are integrated, and closer to the modern agroforestry system, which might be used locally, regionally and nationally as farming packages to other areas.