This study examined the challenges that pre-service teachers faced when implementing inquiry and their perspective on how to overcome them. The data sample was 55 pre-service teachers (PSTs) enrolled into two sections of a science methods course in a private university in North Texas. The data sources consisted of inquiry-based lesson plans, PST interviews, peer teaching observational notes, and field notes to investigate those challenges. The data were coded through designed rubrics for lesson plans and peer teaching sessions and were analyzed using the constant comparative method. The results of this study showed that PSTs faced several challenges regarding the science content and the teaching method. The PST face main challenges with the "explain" and the "elaborate" phases of the 5E. They also faced challenges difficulties with managing the time to teach the 5E model, and mapping the lessons to the different parts of the 5E model. The results also showed several solutions such as having solid science content through engaging in different experiences, and having more practice with the 5E lesson planning. We discuss the implications of this study for teacher education programs.