Value of the data •The reproducibility of the data among samples of different biological replicates demonstrates the reliability of the experimental design, consisting in the artificial in vitro botrytisation of grape berries to study noble rot in controlled conditions. •The RNA-Seq data allow the readers to access to the transcriptomic profiles of both grapevine berries and B. cinerea in conditions of noble rot development from the same samples. •The analysis of differentially expressed genes in both plant and fungus during noble rot provide new data for further meta-analyses using publically available datasets