This paper uses social multi-criteria evaluation (SMCE) as a powerful, transparent and pluralistic methodology for analyzing a complex and conflicting problem: the decision about the approval and adoption of GM cotton farming in Turkey. At this aim, four cotton farming alternatives including business as usual (BAU), ecological farming (ECO), GMO farming (GM) and good agricultural practice (GAP) are evaluated using a set of environmental, social and economic criteria chosen based on an extensive review of cotton and GMO literatures and several in-depth interviews with key stakeholders and experts. Such an analysis showing the socioeconomic and environmental implications of different farming practices and their consequences for different constituencies provide a rich background for policymaking within a multi-layered system of governance. The paper also offers insights to public decision-makers of other potential GMO adopting countries regarding the adoption of GM crops and the allocation of public funds among alternative agricultural practices.