Paper-based microfluidic devices can provide practical analytics platforms for applications such as point-of-care medical diagnostics. So far immobilisation or separation of analytes on such devices has received limited attention. This study introduces inkjet printed polyelectrolyte patterns as possible platforms for immobilisation of cationic and anionic compounds through surface charge interaction. Both cationic (polydiallyldimethylammonium chloride) and anionic (sodium polyacrylate) polyelectrolytes were inkjet printed on a custom designed porous pigment coating, having fine particle internal pore structure to ensure high surface contact between the analytical sample and modified pore walls. Printed polyelectrolyte patterns were themselves largely invisible, including under UV light. In a proof of principle test, a controllable degree of separation of anionic Uranine and Tartrazine dyes from aqueous solution passing through a printed cationic polyelectrolyte region could be observed. However, weakly cationic Rhodamine B could not be captured on anionic regions.