This paper reflects upon cooperative learning integrated in professional learning for students in disciplines of Chemical and Civil Engineering. Outcome Based Education (OBE) has brought a paradigm shift in higher education institutions offering Engineering Education in Pakistan focusing on student achievement and not just instruction by teachers. In this research, spanning over three years, instructional methods were modified in selected courses of Chemical and Civil Engineering both at undergraduate and postgraduate levels to become student-centered, encourage deep learning, and increase student achievement. Multidisciplinary approach towards development of understanding of complex engineering problems is introduced and its results are shared for generating insights. Need to internalize the concept of complex engineering problems is highlighted from the results of the courses taught at undergraduate and postgraduate level using system dynamics methodology. A model for continuous quality improvement is proposed based on the insights gained through observations and feedback.