This paper proposed a methodological framework for the assessment of carbon stocks and the development and identification of land use, land use change and land management scenarios, whereby enhancing carbon sequestration synergistically increases biodiversity, the prevention of land degradation and food security through the increases in crop yields. The framework integrates satellite image interpretation, computer modelling tools (i.e. software customization of off-the-shelf soil organic matter turnover simulation models) and Geographical Information Systems (GIS). The framework addresses directly and indirectly the cross-cutting ecological concerns foci of major global conventions: climate change, biodiversity, the combat of desertification and food security. Their synergies are targeted by providing procedures for assessing and identifying simultaneously carbon sinks, potential increases in plant diversity, measures to prevent land degradation and enhancements in food security through crop yields, implicit in each land use change and land management scenario. The scenarios aim at providing “win-win” options to decision makers through the framework’s decision support tools. Issues concerning complex model parameterization and spatial representation were tackled through tight coupling soil carbon models to GIS via software customization. Results of applying the framework in the field in two developing countries indicate that reasonably accurate estimates of carbon sequestration can be obtained through modeling; and that alternative best soil organic matter management practices that arrest shifting “slash-and-burn” cultivation and prevent burning and emissions, can be identified. Such options also result in increased crop yields and food security for an average family size in the area, while enhancing biodiversity and preventing land degradation. These options demonstrate that the judicious management of organic matter is central to greenhouse gas mitigation and the attainment of synergistic ecological benefits, which is the concern of global conventions. The framework is to be further developed through successive approximations and refinement in future, extending its applicability to other landscapes.