A methodology for the determination of Zn(II), Cd(II) and Pb(II) directly in dissolved honey samples by potentiometric stripping analysis with a flow cell is proposed. Heavy metals in honey are of interest not only for quality control, but can be used also as an environmental indicator. In this work honey samples were collected in different places of Burgos (Spain). Lead (II) and cadmium (II) can be directly determined. It is necessary to avoid the Zn–Cu interference for zinc (II) determination by adding Ga(III) in the adequate concentration, which has been calculated by using an experimental design methodology. The results were compared with inductively coupled mass plasma spectrometry as reference method.