An original approach based on successive size-exclusion and hydrophilic interaction HPLC (HILIC) was developed to purify traces of Ni species from a plant aqueous extract. The degree of purity achieved was for the first time sufficient for the identification, in a natural sample, of a number of non-covalent metal complexes by electrospray Q-TOFMS/MS. Nickel complexes with malate, citrate, histidine, EDTA and nicotianamine (NA) were identified in the roots, xylem, shoots and their protoplasts of a metal hyperaccumulator plant Thlaspi caerulescens. The quantitative recovery of the most stable of these complexes (with EDTA and NA) allowed their quantitative determination by SEC-ICP-MS.