Globalization has interaction on each and every connection of life, people. Higher education is not an exception from these transformations. Effects of globalization on higher educational institutions (HEIs) include student mobility, faculty exchange, research, rankings, academic collaborations, diverse cohorts and international enrolments. Globalization also brought isomorphic pressures on HEIs to become equivalent and comparable. This paper discusses isomorphism which leads to Indian universities becoming more homogenous and thus consequently loosing autonomy and in turn individual identity. Secondly, it discusses the constraints on academic autonomy of new HEIs due to peer pressure isomorphism. with their academic autonomy. This report is based on university affiliated HEIs which opted autonomous status under the new schemes and policies. In this report two case studies, Government College of Engineering, Pune and MIT Academy of Engineering, Pune, are presented.