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• Fruits from wastewater-irrigated tree are exempt of fecal-borne pathogens. • Shoot and fruit endophytic bacteria increased in wastewater-irrigated trees. • Transpiration increased shoot endophytic bacteria in wastewater-irrigated trees. • Soil total coliforms and total bacteria counts were unaffected by wastewater. • Soil E. coli was found at low concentrations in wastewater-irrigated trees. Irrigation with wastewater can be a solution to preserve and mitigate freshwater demand, in particular during drought periods. Unfortunately, wastewater, although being treated at different levels, could be a carrier of human pathogens (e.g., E. coli) and potentially contaminate crops for human consumptions. This study investigated the seasonal microbiological concentrations, on soil, shoot and fruit tissues of potted peach trees, following two irrigation treatments: freshwater (FW) and secondary urban wastewater without the final disinfection treatment (SW). E. coli was only detected in SW irrigated soil, whereas total coliforms (TC) and total bacteria counts (TBC) were similar in both treatments throughout the season. Endophytic E. coli, Salmonella spp. and TC were not detected in shoot and fruit, but a higher presence of total bacteria (TBC) was observed in SW-irrigated tree compared to FW-irrigated tree. In particular, SW shoots had a higher load compared to fruits, thus showing a potential effect of leaf transpiration, that promoted the transfer of water-borne bacteria from soil to the epigeal part (shoot). The adoption of low-quality SW (even above the microbiological limits of the European Regulation 2020/741 for wastewater re-use in agriculture), when a drip irrigation method is applied, could be a valid alternative to save fresh water without compromising fruit safety. [Display omitted] [ABSTRACT FROM AUTHOR]