This study reports on the microbiological quality of fresh and laboratory prepared pitaya fruit juice compared this with those collected from street vendors in the Penang island of Malaysia. Additionally, the microbial growth patterns were monitored during extended storage for up to 7 days at 2 different temperature ranges (at 10°C and 25±1°C). Results revealed the presence and increase in the incidence of bacteria, yeasts and moulds in all the juice samples (fresh and stored). Except for Klebsiella pneumoniae all the other foodborne pathogens screened in this study such as: Staphylococcus aureus, Salmonella sp. and generic Escherichia coli were absent. Our results highlights and stresses the need to employ proper hygienic conditions during harvesting and processing stages of pitaya fruit or their juices to improve the overall microbial quality to ensure adequate safety for consumers.