This contribution observes changes in the participation of the individual classes of bourgeois society in town administration and the formation of its independent policy towards the sovereign and other groups of Estates’ society in the period between the Hussite Revolution and the defeat of the Estates’ Rebellion in 1620, against the backdrop of several socio-political crises in Prague (namely in The Old Town and The New Town of Prague). It does not study merely the periods of these crises but it primarily pays attention to the consequent periods of relative stabilization of social conditions. It searches for answers to the question to what degree certain „democratic“ features of the system of functioning of the administration in both towns of Prague were maintained and in which direction they developed. Indeed, they significantly influenced the functioning of the system of municipal administration from the period of the Hussite Revolution onwards. The formation and functioning of the early modern administration of the Boroughs of Prague is viewed in the context of Central European development (respectively, the development of the Holy Roman Empire and Imperial towns) as a process of communication between the three fundamental components of municipal administration, i.e. a municipal community, town elders and a council, at the level of administration, as well as at political, religious and economic levels.