Models influence the teaching and learning of chemistry and thereby influence the perception of the scientific phenomenon. Our study is focused on the middle school teachers’ dilemma about developing and using models in chemistry learning, using the Project-Based Inquiry Science (PBIS) Air-Quality science-curriculum module. PBIS Air-Quality is a case-study based module that supports learning chemistry through Project-Based Inquiry and Learning by Design approaches. Furthermore, middle-school students are also facing hardships in constructing models of abstract concepts. The research goals are to (a) investigate the gap in teachers’ approach to “developing and using models” in the chemistry classroom in comparison with the description in documents “A framework for K-12 Science Education", National Research Council (NRC), 2012 and Next Generation Science Standards (NGSS), 2013 and (b) investigate middle-school students’ ability of developing and using models for scientific understanding in the context of PBIS Air-Quality module. Our research questions are 1. Do teachers’ perceptions of the scientific practice “developing and using models” differ from how it is conceptualized in the framework of NRC and NGSS and in what aspects? 2. What are the characteristics of students’ competency to develop and use models in the context of learning PBIS Air-Quality module and can it be associated with the teachers’ perception of this scientific practice? Participants include five middle school teachers who taught chemistry in the context of PBIS Air-Quality module and 347 grade eight students. We apply the mixed-methods approach. The qualitative part includes semi-structured teachers’ interviews and the quantitative part includes pre and post students’ questionnaires and drawings of air before and after the study of the Air-Quality module. The contributions of our study are identifying the gap in the teachers’ perceptions of developing and using models and misconceptions held by students in learning chemistry.