The effectiveness of a water-assisted UV-C (WUV) technology for the decontamination of fresh-cut broccoli from conventional and organic agricultural practices was evaluated as an alternative to chlorine sanitation. Several WUV doses (0.3–1.8 kJ m−2) were tested alone or combined with peroxyacetic acid (PAA). Results showed that 0.5 kJ m−2 was sufficient to reduce natural total aerobic mesophilic microorganisms by 2 log10 in conventional broccoli without negative consequences on the physical quality. However, in order to achieve the same effect on organic broccoli, a combined application of at least 0.3 kJ m−2 and 50 mg L−1 PAA was required. Total antioxidant capacity (TAC) was enhanced by 42, 90 and 81% in conventional broccoli 24 h after treatment with 0.3, 0.5 and 1.8 kJ m−2, respectively, compared to water-control. A similar trend was observed in organic broccoli, although the increase in TAC (by 22%) compared to the water-control was only significant when a dose of 1.8 kJ m−2 was used. Similarly, 0.5 kJ m−2 enhanced the sulforaphane content in conventional broccoli by 1.5 and 4-fold compared to water and chlorine-controls, respectively. WUV is a promising alternative technology to improve the microbiological and nutritional quality of fresh-cut broccoli.