Rapid urbanization has aggravated the challenges in sustaining the peri-urban rice farming sector. The challenges arising from rapid urbanization are threatening rice farmers in peri-urban areas due to increasing economic and land pressures. This has caused a significant marginalization among rice farmers. In Indonesia, despite contributing 13.28% of the national GDP in 2021, the agricultural sector is dominated by marginal farmers who struggle with poverty and lack of land ownership. This study aims to identify different pathways for marginalization of rice farmers by integrating spatiotemporal land use and land cover (LULC) change analysis, landscape fragmentation metrics, and system dynamics through causal loop diagrams (CLD). Furthermore, the redefinition of the term marginal rice farmers is done by considering the total cultivated rice field and broader factors that contribute to the self-reinforcing loop of marginalization. This study shows that rice farmer marginalization in peri-urban areas is caused by small land size or poverty, and reinforcing feedback between ecosystem service degradation, productivity decline, economic pressure, and land conversion that interact differently across landscape configuration. Moreover, this study enhances the understanding of peri-urban agricultural transformation and provides landscape-sensitive policy insights to support inclusive and resilient agricultural systems by reconceptualizing marginalization of rice farmers as a dynamic socio-spatial process.