Abstract Trawl bans are relatively uncommon, particularly at the level of an entire coastal jurisdiction, and have seldom been studied in the tropics. A permanent territory-wide trawl ban has been implemented in Hong Kong coastal waters since the beginning of 2013. We used isotope-based metrics, in addition to traditional community measurements, to determine whether benthic crustacean assemblages had shown any signs of recovery three years after the trawl ban. We expected increases in species richness, abundance and biomass as well as shifts in trophic structure, including longer food-chain length (FCL) and greater trophic diversity after the ban. We further anticipated that carnivorous crustaceans would have higher mean trophic positions (MTPoC) at the assemblage level, and broader trophic niches at the species level. Sampling was undertaken at six sites in three regions (eastern, western and southern waters) before (in 2012) and after (in 2015) the ban. In general, there were no changes in assemblage total abundance or species richness after the trawl ban, but a decrease in biomass was observed. Isotope-based metrics showed that trophic niches of the crustacean assemblages were, however, broader at all sites after the ban. The FCLs at four sites in the eastern and western waters were longer after the ban, and three of them also showed increased MTPoC. In contrast, declines in FCL and other trophic metrics were recorded at the two southern sites. Among the five most abundant carnivorous crustaceans, all species at one eastern site, three at one western site, and four at three other sites expanded their trophic niches after the trawl ban; no changes were evident at the other eastern site where carnivores were scarce. By using isotope-based trophic metrics, we detected early functional recovery of the crustacean assemblages that cannot be revealed by traditional community analyses, implying that the effectiveness of the trawl ban would be underestimated if the assessment was based on community measurements only. We, therefore, advocate the use of isotope-based trophic metrics in tandem with the community measurements for more comprehensive assessments of ecosystem responses to anthropogenic disturbances and management interventions designed to alleviate them.