We investigate the interactions between natural resource-based poverty traps and food security for smallholder farms in highland Kenya using a recently developed system dynamics bio-economic model. This approach permits examination of the complex interactions and feedback between farm household economic decision-making and long-term soil fertility dynamics that characterize persistent poverty and food insecurity among smallholders in rural highland Kenya. We examine the effects of changing initial endowments of land and stocks of soil organic matter on smallholders’ well being, as reflected in several different indicators. We show that larger and higher quality land endowments permit accumulation of cash and livestock resources and conservation of soil organic matter relative to smaller or more degraded farms. This suggests the existence of asset thresholds that divide food secure households from food insecure ones.