The oil of Persian lime (Citrus latifolia) seed was extracted using three methods (cold-pressing, solvent extraction and enzyme-assisted aqueous extraction using Protamex and Celluclast) to compare the effect of extraction method on oil quality through trace metal elements (Fe, Cu, Ni, Co, Pb and As) content. The results demonstrated that extraction method significantly (P < 0.05) influences the trace metal elements content of oil. The reduction pattern of Fe > Cu > Ni > Co > Pb > As was observed in Persian lime seed and extracted oil samples. The highest concentration (mg/kg) of iron (7.3272 ± 0.0263), copper (0.350033 ± 0.00153) and lead (0.00891 ± 0.00003) were observed in cold pressed oils. The oils extracted using enzyme-assisted aqueous extraction method showed the highest concentration (mg/kg) of nickel (0.069855 ± 0.000167) and cobalt (0.054555 ± 0.000163). Arsenic was not detected in seeds and any of the extracted oil samples. The concentration of Fe (3.0363 ± 0.0423 mg/kg) and Cu (0.280167 ± 0.00151 mg/kg) as a pro-oxidant was lower in the Persian lime seed oil obtained by enzyme-assisted aqueous extraction method.