Lowland tropical forests are subject to intensive land use changes, and successful management requires that ecosystem services be incorporated into landscape management. In two pilot study sites in East (E) and Peninsular (P) Malaysia, we conducted a risk assessment of ecosystem degradation and found that the development of oil palm plantations and shifting agricultural practices are important factors in P Malaysia and E Malaysia, respectively, causing a degradation in carbon stocks and biodiversity. Based upon the results, we developed land use zoning plans by placing a green corridor in the P Malaysia site and a buffer zone in the peripheral area of the national parks in E Malaysia, which will eventually meet the goal of REDD plus (reduction of emissions from deforestation and degradation). In the P Malaysia site, as a practice test of the REDD plus goals, we started developing the green corridor by planting native, orchard trees in riverine areas inside the oil palm plantation. In this paper, we report the effects of the green corridor on biodiversity and carbon stocks, considering the revenue earned on the CO2 market and the maintenance cost of the corridor. We also consider the importance of local participation and governance for land use management with respect to financial incentives (such as REDD plus) that are expected to sustain long term remediation activities.