The Indian academic system is in a period of rapid transition, evidenced by the increasing number of higher education institutions, students and academics. However, very few studies have explored academics’ research productivity and the various factors influencing it. Even those few studies have largely ignored the influences of indigenous factors and academic dishonesty on research productivity. Using a mixed-method approach, this research explores how the changing academic environment influences academics’ research productivity in South Indian engineering institutions established after 1990. Important demographic factors influencing research productivity have been identified. The results show that indigenous factors play a major role in motivating the academics to conduct research, whereas corruption / academic dishonesty, thought to be prevalent at all levels in the higher educational system, tend to reduce their research motivation. The research shows the complex interconnections between the changing academic environment, indigenous factors and academic dishonesty, and their influence on academics’ research. The results of this work can be used for informing future higher education policy-making in terms of increasing research productivity and decreasing a range of academic dishonesty in the context of a rapidly changing academic system.