In the context of climate change, a nutritional transition, and increased pressures to migrate internally and internationally, this study examined the relationship between seasonal food insecurity and demographic, socioeconomic, and agricultural production factors among small-scale subsistence farmers in rural northern Honduras. Anchored by a partnership with the Fundación para la Investigación Participativa con Agricultores de Honduras (FIPAH) and the Yorito Municipal Health Centre, a cross-sectional household survey was administered in Yorito, Honduras, in July 2014. The study population included 1263 individuals from 248 households across 22 rural communities. A multivariate mixed effects negative binomial regression model was built to investigate the relationship between the self-reported number of months without food availability and access from subsistence agriculture in the previous year (August 2013-July 2014) and demographic, socioeconomic, and agricultural production variables. This study found a lengthier 'lean season' among surveyed household than previously documented in Honduras. Overall, 62.2% (95% confidence interval (CI): [59.52, 64.87]) of individuals experienced at least four months of insufficient food in the previous year. Individuals from poorer and larger households were more likely to experience insufficient food compared to individuals from wealthier and smaller households. Additionally, individuals from households that produced both maize and beans were less likely to have insufficient food compared to individuals from households that did not grow these staple crops (prevalence ratio (PR) = 0.83; 95% CI: [0.69, 0.99]). Receiving remittances from a migrant family member did not significantly reduce the prevalence of having insufficient food. As unpredictable crop yields linked to climate change and extreme weather events are projected to negatively influence the food security and nutrition outcomes of rural populations, it is important to understand how demographic, socioeconomic, and agricultural production factors may modify the ability of individuals and households engaged in small-scale subsistence agriculture to respond to adverse shocks.