At the onset of the COVID-19 pandemic, Indonesia announced major higher education (HE) policies called Kampus Merdeka and launched the Mid-Term National Development Plan and the Strategic Plan of the Ministry of Education and Culture. While none of these policies anticipated the pandemic, two aspects of the policies have been somewhat accelerated by the pandemic, though not without problems. These are: greater autonomy for state HE institutions and proliferation of distance/online education. The pandemic provides a greater autonomy for most state HE institutions to manage their education services. However, they are increasingly drawn into the governments’ public health campaigns, exerting their facilities and human resources. Seemingly, the autonomy of HE institutions has to be in compliance with government agendas. While HE institutions throughout the archipelago instantly shifted into online learning due to the pandemic, to what degree online learning can be a permanent feature of Indonesian HE is still questionable. The chapter ends with an examination of the possible landscape of the Indonesian HE sector post-COVID-19 and the remaining challenges.