Magnetic beads (Dynabeads$^{(R)}$) embedded in ~1 micron size polystyrene beads bearing surface carboxylic acid groups were modified with aminobenzyl ethylenediaminetetraacetic acid (ABEDTA) to concentrate or separate metal ions using pH gradients on micro and nano scales. The immobilization of ABEDTA was achieved by amide formation. The presence of the metal chelating functional group in the fully deprotonated form was confirmed by FT-IR. The chelation efficiency of beads was tested by determining metal ions in supernatant using GFAAS when pH gradients from 3 to 7. Mixtures of Cu and Mg and of Cd and Mn (at 10 ng/mL of metal) were separated as the difference in formation constant with the functional group of ABEDTA. The separation was repeated twice with relative standard deviation of <18%. A polydimethylsiloxane (PDMS) microchip column packed with EDTA-coated magnetic beads was optimized to concentrate metal ion for practical applications by eluting a Cu solution of micro scale at pH 3.