CONTEXT Over the past two decades, the Mekong region has experienced significant transformation of its agricultural sector from subsistence farming to export crops driven by the expansion of agricultural land and of irrigation, plus intensification thanks to mechanization and the use of chemical inputs. In the context of agrarian transition, maintaining “organic by default” rice farming systems that do not rely on chemical inputs, is challenging. OBJECTIVE Based on a case study in Preah Vihear, the organic province of Cambodia, this paper examines whether organic rice certification can maintain “organic by default” practices in a context of unprecedented agricultural intensification. METHODS Using agrarian diagnosis, we investigated the impacts of an organic rice certification scheme on the future of organic rice-based farming systems. We built a functional typology of five farming systems that co-exist in the study area to understand the roles of organic rice in each system. RESULTS AND CONCLUSIONS From an economic perspective, organic rice is less profitable than recently introduced cash crops, e.g. cassava, cashews. The positive impact of certification of organic rice is threatened by lock-in factors, e.g. labor diversification in both farming and non-farming activities, cash flow management, the certification process, leading farmers to abandon organic rice for cash crops for export. We discuss the key role of agricultural cooperatives in the certification process of organic rice. SIGNIFICANCE The paper questions the capacity of a certification scheme to keep up with the process of intensification that undermines the profitability of the remaining “organic by default” rice systems. Beyond the significance of the results in the study area, one of the last strongholds of traditional rice systems in Cambodia, the paper illustrates the disappearance of “organic by default” rice systems in the whole country as well as in the Mekong region.