The retention of underrepresented students remains a significant challenge in the STEM (Science, Technology, Engineering and Math) disciplines. A broad range of studies across several disciplines have shown that conventional approaches to STEM instruction may have been unintentionally exclusive to students whose ethnicities are not traditionally represented in the STEM fields. This 'exclusive' classroom atmosphere has emerged as a major reason for the attrition of underrepresented minority students from STEM majors. In this manuscript, I describe a conceptual model called Deep Teaching, describing how pedagogical transformation incorporating practices that are more inclusive can occur. The model marks an evolution from other frameworks advancing inclusive instruction in higher education by advocating for the primacy of Freirean philosophy when thinking about self and student. Using specific examples, I discuss how a sequential approach to understanding ourselves and empathizing with students puts the instructor in a better position to create enduring, positive classroom climates. I also describe considerations necessary for various contexts, and suggestions for continued commitment to inclusive pedagogy in the long-term.