Pb(Zr,Ti)O3 (PZT) is a ferroelectric material interesting for its high dielectric constant and piezoelectric response. PZT thin films can be prepared by various methods, e.g. pulsed laser deposition, chemical vapor deposition, sol-gel and, most frequently, sputtering. Though the magnetron sputtering is used more frequently, PZT thin films can be prepared also by ion-beam sputtering (IBS). In this paper we study the deposition process of PZT thin films in our IBS system with a possibility of ion-beam assisted deposition (IBAD), which has the advantage that more energy can be added to the growing layer. We show how in our system the resulting layers, mainly their quality, the Pb content, which is important for the creation of the perovskite crystal structure, and the resulting crystal structure are influenced by the oxygen flux during the deposition for the samples grown on the silicon substrate with and without an intermediate Ti seeding layer.