The intervention study presented in this paper explored pre-service science teachers' (PSSTs) understanding of scientific inquiry (SI) and scientific practices (SPs) during a laboratory application in science education course. Thirty-nine secondary school PSSTs, who study in the Science Education Department in a public university in Turkey, enrolled in a 14-week-long course and volunteered to participate in the study. The participants were exposed to a method is called "the 4-phase implementation" that includes laboratory-based inquiry activities addressing SI and SPs and they completed microteaching presentations. Their understanding of SI and SPs was examined through the course period. The main data sources included "Views about Scientific Inquiry (VASI) Instrument" and concept maps were used to track the changes in these understandings. The findings indicated that PSSTs had inadequate understanding of inquiry on some aspects even after the treatment. Yet, the method had positive impact in PSSTs' understanding inquiry especially in terms of facilitating the comprehension that scientific investigations begin with questions, there is no single method in investigations, and explanations are derived from collected data. The concept maps created by some of the participants also supported these results and revealed a more coherent and holistic understanding of SPs by integrating both epistemic and social components into their maps. However, PSSTs did not seem to have totally understood other aspects of inquiry including the inquiry procedures, the research conclusions, and the difference between data and evidence. Further implications are critically discussed in terms of designing future laboratory applications for science education courses.