Renewable energy sources are essential to mitigating climate change, with biofuels offering a sustainable alternative to fossil fuels by reducing greenhouse gas emissions. Jatropha curcas, the best, non-edible, high-oil-yielding species, is a leading candidate for biodiesel production. However, ensuring a stable seed supply through effective storage is critical for biodiesel markets stability. This study evaluated the physiological and biochemical viability of J. curcas seeds stored at 4 °C with controlled humidity using 1.5 g of silica gel per gram of seed over 12 months. The results demonstrated that low-temperature, low-humidity storage significantly reduced metabolic activity, embryo respiration, and seed deterioration, preserving high germinability and oil quality. Despite a slight increase in mean germination time, seeds retained resilience in germination potential and viability. Additionally, preliminary assessments of salt tolerance revealed the potential of J. curcas seeds to germinate under saline conditions, supported by analyses of mineral nutrition and salt tolerance-related gene expression. These findings underscore the practicality of optimized storage conditions for maintaining seed quality and economic value, ensuring a consistent supply chain for biodiesel production. This study highlights the importance of integrating storage strategies into biodiesel systems to enhance sustainability and market resilience in the face of fluctuating production demands.