In the agriculture sector, sustainability retention of biomass management is a complicated issue, especially without increasing potential damage towards the environment. This study aims to develop an integrated MAGI conceptual framework using Material Flow Analysis (MFA) and Geographic Information System (GIS) to measure and display spatial biomass energy flow in an agricultural system in Kuala Terengganu. The scope for this research consists of two dominant pools namely crop production and livestock production. By integrating the MFA inventory data, biomass energy model for the year 2016 has been developed based on early results obtained. The study found that the major portion of the energy is focused in crop production, which is 56% higher than livestock production. The findings also estimated 35% agricultural waste recovery potential It seems that the integration of MFA and GIS is an interesting, ideal, and powerful combination of decision making tool because it is able to provide information and firm decision on the development of bioenergy management system and can be used to implement strategies to reduce energy use and pollutants released into the environment.