Perennial plants reproduce through a high interannual variability in seed production, with irregular years of high reproductive output—a phenomenon known as mast seeding or masting. While mast seeding is linked to fluctuations in weather and resource availability, the molecular mechanisms that trigger or suppress flower production remain poorly understood. Here, we explored molecular basis of tree flowering, and relationships between gene expression and environment. We collected a unique nine-year dataset of seasonal gene expression from leaf samples of Japanese beech (Fagus crenata) at Mt. Naeba in central Japan. From a total of 40,000 genes, we identified 20 genes whose expression levels were associated with heavy flowering, including key floral regulators and additional genes related to sulfur deficiency. Nitrogen has previously been shown to be a key trigger of flowering in F. crenata. We found that increased nitrogen availability elevates sulfur demand, and when sulfur supply fails to keep pace, plants experience sulfur limitation and activate a low-sulfur response that suppresses flowering. These findings provide new insights into how seasonal molecular regulation of tree flowering shapes reproductive phenology and its relationship with resource availability.