The blue swimmer crab, Portunus pelagicus, is an edible abundant crustacean found in many seas around the world, including the Arabian Gulf. In this study, the concentrations of six metal ions in the white and brown meats of P. pelagicus from four sites in Bahrain were determined. P. pelagicus was found to accumulate Zn2+ and Cu2+ higher than other metal ions in the order of Zn2+ > Cu2+ > Cd2+ > Ni2+ > Cr3+, while Pb2+ was not detected. The overall average concentrations of Zn2+, Cu2+, Cr3+, Ni2+, and Cd2+ in white meat were 236.2, 69.5, 0.109, 0.159, and 0.273 mg/kg, while in brown meat, they were 235.4, 199.2, 0.133, 1.25, and 4.87 mg/kg based on dry weight, respectively. Concentrations of Pb2+ and Cd2+ were safe according to Bahrain's and European Commission guidelines. The estimated weekly intake (EWI) values of Zn2+, Cu2+, Pb2+, and Cd2+ via consumption of crab's white meat (edible tissue) were 102.1, 30.1, 0.042, and 0.12 µg/kg/week, respectively, which are far lower than the maximum recommended values established by the FAO/WHO. The hazard quotient (HQ) values of individual trace metal ions and the synergistic effects of total trace metal ion (hazard index) were below 1, indicating that there is no potential health risk on the consumption of crab edible tissues (white meat). However, elevated levels of Cd2+ (0.05-1.73 mg/kg wet weight) in the brown meat (hepatopancreas) were detected. The female P. pelagicus accumulated high levels of Zn2+ and Cu2+ in the white meat, as well as Cu2+ in the brown meat compared to males. Additionally, it was found that Cu2+ and Cd2+ were significantly higher (p < 0.05) in brown meat compared to white meat. Higher concentrations (p < 0.05) of Zn2+, Cu2+, and Cd2+ were observed in crabs collected from sites that have harsher environmental conditions.