This study aims to examine the perceptions and practices of socioscientific issue- (SSI) based teaching of 37 pre-service science teachers (PSTs) studying for a master's degree in science education as well as the factors affecting their SSI-based teaching during their field experience in the first semester of the academic year 2014. Data were collected through open-ended questionnaires, focus group interviews, semi-structured interviews after actual practices, and informal interviews and by observing video recording of PSTs' SSI-based teaching. The collected data were analysed using an inductive data analysis. The findings show that while most PSTs' perceptions did not relate to their practices of SSI-based teaching, few teachers had SSI-based teaching perceptions that were consistent with their practices, which emerged under three themes: promoting students' higher-order thinking, focusing on the scientific content/concept dimensions of SSI, and promoting students' awareness of the personal and social impacts of science. In addition, we found that there were two ways of using SSIs in classrooms: a one-period and an entire unit SSI-based teaching. The key factors affecting their SSI-based teaching included knowledge of SSI-based teaching, managing related discussions and content regarding SSIs, and the availability of time. These findings have implications for PSTs who adopt SSI-based teaching methods in their classrooms.