Glomalin-related soil protein (GRSP) is recalcitrant compound in the soil and sediment and plays a crucial role in metal transportation. However, potential metal speciation changes during GRSP extraction remain unreported. Here, a feasible GRSP extraction and purification procotol is described for robust determination of GRSP-bound metal(loid)s. Several spectrum patterns measured before and after GRSP extraction indicate that the GRSP extraction process does not significantly affect the mineral state of the samples. Potential bias generated by simultaneous metal release during GRSP extraction can be effectively eliminated by applying complete and independent dialysis.•Na signal appeared in the X-ray photoelectron survey spectrum after GRSP extraction, suggesting that Na exchange may be a critical process in releasing metal(loid)s.•Element maps obtained using secondary ion mass spectroscopy exhibited different distribution of C-N and Fe after GRSP extraction, thus suggesting that uncoupling of the Fe-organic framework occurred during GRSP extraction, which could result in the release of organic matter and metal(loid)s.•European Community Bureau of Reference (BCR) subsequent extraction reveals that most of the metal(loid)s were extracted from the acid-exchangeable and residual fraction during GRSP extraction. Remarkable differences in the GRSP-bound metal content before and after dialysis implied that the dialysis could remove most metal(loid)s.