Yttria-stabilized zirconia thin films for micro solid oxide fuel cell applications were grown by pulsed laser deposition onto silicon-based microfabricated substrates. In order to obtain pinhole-free membranes, the influence of the microstructure of the target on the ejection of particulates to the film was studied. Targets with different contents of yttria (3 mol% Y2O3: ZrO2 and 8 mol% Y2O3: ZrO2) and fabricated by different sintering methods (conventional sintering and spark plasma sintering) were evaluated. Microstructural and electrical properties of targets and deposited membranes were evaluated concluding that the use of targets with smaller yttria content and grain size, with expected better mechanical properties, drastically reduces the particulates in the membranes without significant effect on the resistance. 3 mol% Y2O3:ZrO2 targets prepared by spark plasma sintering have been proven to provide almost pinhole-free membranes.