High throughput transcriptomic studies (microarray, RNA-seq) are powerful tools to decipher changes in gene expression during fruit development and to target candidate genes involved in the plant response to environmental stresses. However, the rapid RNA turnover rate constitutes a major drawback in transcriptomic studies upon introducing sensitivity to environmental and trophic changes within one day. Thus, their precision and reproducibility highly depends on the sampling protocol. The present study aimed to test the hypothesis that fast transcriptomic changes induced by heat stress may vary during the day in microvine berries. Berry development was characterized with whole genome microarrays on microvine plants grown under fully controlled environment. Developmentally regulated transcripts could be clustered the same way independently at day and night with 20 % more transcripts identified during the night. Strikingly day-night regulation varies to a high extent between green and ripening berries. Interestingly, an important shift in the day-night regulation of secondary metabolism was observed from green to ripening berries. For the first time, the present study revealed important circadian mechanisms related to secondary metabolism changing throughout fleshy fruit development