Background: Flipped classrooms are increasingly becoming popular as a pedagogical method to improve student engagement, critical thinking skills, learning outcomes and success. However, current literature on flipped classrooms provides limited insight on instructors’ motivations, perceptions, and challenges, especially in the context of higher education. Purpose: The purpose of this qualitative study was to understand the instructors’ motivations to adopt the flipped classroom method and the challenges and issues that instructors faced when they taught in a flipped format at a south central urban public university. More specifically, this study noted the best strategies and technologies for implementation of flipped classrooms. Methods: This study used a semi-structured interview method outlined by Phil Carspecken for critical qualitative research. Six faculty instructors who previously taught using a flipped class method were interviewed. The data were analyzed using reconstructive, more specifically high and low level coding to draw out the themes. Peer-debriefing was used to increase trustworthiness of analysis. Results: The findings of this study revealed several interconnected themes related to the research questions: (1) the need for creating student-centered, active learning pedagogy, (2) lack of clear understanding of the “flipped” format on the part of the students, (3) the changing nature of student responsibilities and the instructor’s role in a flipped class setting, (4) the strategies for accommodating the diversity of the students’ knowledge bases, and creating engagement and assessment tools, (5) importance of creating proper communication strategies and dealing with unpredictable technology issues. Conclusion: The findings can potentially serve as a guide for other instructors who want to adopt flipped classroom method to improve their students’ learning outcome.