Restoration science is incentivised by the valuable functions and services provided by coastal ecosystems such as mangroves. However, environmental contaminants can have detrimental effects on ecosystems, threatening the very benefits that restoration seeks to enhance. Despite this, sediment chemistry, and the effects of contaminants, are rarely considered when restoring mangroves. To evaluate the risk of restoring mangroves in contaminated environments, this study assessed the influence of sediment chemistry on contaminant bioaccumulation in shore crabs from restored and natural mangroves. This was complemented by characterisation of the crab metabolome, to investigate the sub-lethal effects of contaminants on shore crab physiology. There were significantly greater concentrations of several trace elements, PAHs, and PFAS compounds in both the sediment and crab tissues collected from the restored contaminated site compared to those from the natural control site. Differential metabolome profiles amongst the three crab populations indicated potential impacts to physiological status that may affect overall metabolic health. This suggests that the restoration of contaminated environments could create ecological sinks, where animals take residence in a poor-quality habitat, their health is impacted, and populations decline. This study highlights the importance of considering, and at times mitigating, contaminant burden on urban ecosystems when restoring mangrove wetlands.