This study examines how pre-service elementary teachers (PSETs) view inquiry-based science learning and teaching, and how the science methods course builds their confidence to teach inquiry science. Most PSETs think that inquiry is asking students questions rather than a formal set of pedagogical tools. In the present study, three groups of PSETs (n = 14, 20, 20) were included. For each group, pretest and posttest attitudes and knowledge base were assessed using a 32 item questionnaire combining twenty-six Likert-type and six open-ended questions as well as half-hour semi-structured one-on-one interviews. Results from the pretest questionnaires showed that most PSETs had simplistic views of inquiry-based teaching. The instructor was able to modify the science methods course (the intervention phase) to focus on the concepts of science-based inquiry teaching that were shown to be lacking in the PSETs' knowledge base. The analysis of the post-test questionnaire showed significant increase on 17 of the 26 Likert-type questions reflecting increases in PSETs' understanding of inquiry-based teaching. The study shows PSETs' understanding of inquiry-based science teaching is a key step to build their confidence and efficacy of teaching science.