As the world’s largest predominantly Muslim country, certain Muslim communities in Indonesia believe that the Jakarta Charter is an effective bridge to realise Islamic sharia due to its virtuous historical values. However, the aim is not reached yet, as major Muslim groups and main political forces in the parliament assume that the Charter is no longer relevant with current circumstances. This paper is an attempt to examine political thoughts of the elites in Muhammadiyah, the most influential Muslim-moderate organisation in Indonesia, towards the notion of the establishment of Islamic sharia by applying the Jakarta Charter as the state principle during transition era particularly surrounding the annual session of the People’s Consultative Assembly (MPR) 1999-2002. Indeed, elites in Muhammadiyah have a significant role to maintain the present and future political trajectory. Thus, it is a fascinating study to depict contemporary thoughts of the Muslim elites. As a result, the paper found three models of political thoughts in Muhammadiyah namely the moderate-transformative, the moderate-realistic, and the accommodative-pragmatic. Each thought has its features and reasons. In sum, the paper eventually demonstrates that no one the elites in Muhammadiyah encourages the concept of the Islamic state.