Seed of Shismus arabicus, a desert annual, display a seasonal tolerance to dehydration. The occurrence of a metabolic seasonal rhythm and its relation with the fluctuations in seed dehydration tolerance was investigated. Results: Dry seeds metabolism was the least affected by the season, while the metabolism of germinated and dehydrated seeds exhibit distinct seasonal patterns. Negative associations exist between amino acids, sugars and TCA cycle intermediates and seed survival, while positive relations exist with seed germination. In contrast, associations between the level of secondary metabolites identified in the dehydrated seeds and survival percentage were evenly distributed in positive and negative values, suggesting a functional role of these metabolites in the establishment of seed dehydration tolerance. Conclusion: Our results indicate the occurrence of metabolic biorhythms in germinating and dehydrating seeds associated with seasonal changes in germination and, more pronouncedly, in seed dehydration tolerance. Increased biosynthesis of protective compounds (polyphenols) in dehydrating seeds during the winter season at the expenses of central metabolites likely contributes to the respective enhanced dehydration tolerance monitored.