Botrytis cinerea, is one of the major causal agents of postharvest decay in table grapes, contributing to 20% losses world-wide. The aim of this study was to determine the prevalence of B. cinerea at different phenological growth stage (full bloom, pea size and fully mature berries) and the impact of agro-climatic sites on pathogen incidence. Droplet digital polymerase chain reaction (ddPCR) was used simultaneously with culture based methods to detect and quantify B. cinerea. Botrytis cinerea was detected at different phenological stages on asymptomatic grape samples. Prevalence and level of B. cinerea differed between phenological stages and sites. Full bloom stage of site B showed the highest prevalence of B. cinerea (82.9%) compared to site A (33.3%). For the latter phenological stages (pea size and mature stage), site A had the highest prevalence (100% for both), compared to 35.2% and 44.4% observed at site B, respectively. Furthermore, the B. cinerea concentration varied between stages within the two sites. The concentration of B. cinerea at site A showed a threefold increase from pea size (2.67 copies μL−1 of DNA) to mature berry stage (9.16 copies μL−1 of DNA), compared with the decline noted for similar growth stages at site B. Botrytis cinerea inoculum build up on asymptomatic grapes could be effectively monitored as the berry develops at critical phenological stages. Preharvest monitoring of the pathogen can help growers improve well-established cultural and management practices, hence limit the risk of postharvest decay.