Here are some relevant excerpts from Helen Saradi's chapter "Towns and Cities" in the Oxford Handbook of Byzantine Studies, outlining the significant changes in the administration of Byzantine cities over time. The bold text is my own emphasis. This first part is referring here primarily to the early Byzantine period:
Bishops as the spiritual leaders of the urban communities naturally rose to positions of power in the cities. They took initiatives in times of war, appealed for imperial intervention to address urgent civic needs, and took care of civic works, the maintenance and construction of civic buildings (Avramea 1987 and 1989; Feissel 1989; Liebeschuetz 2001a: 137-68). The bishop, together with influential members of the local communities (protoi, proteuontes—headmen; ktetores—patrons), formed a group responsible for appointing civic officers, such as the curator, the sitones
(in charge of corn supplies), the pater, and the defensor (ekdikos). The appearance of these new leaders in the cities was a response to the decline of the decurions (bouleutai) and of the institution of the boule. Although their role in the cities was sanctioned by imperial legislation, the group of new urban leaders was not defined as an institution, as was the boule: the new administrative system was not uniform everywhere in the empire and lacked the formality of the earlier government by the boule (Liebeschuetz 2001a: 104-36; Saradi 2006:151-85).
This was followed by centuries of urban decline to the point that many cities were effectively abandoned. The theme
system took on greater and greater importance until cities re-emerged later on:
From the ninth century, and perhaps already from the late eighth century
(Bouras 2002:501), Byzantine cities were marked by an economic revival. New cities
and towns are mentioned in the sources. In many cases, this was the result of an
imperial initiative. Civil and ecclesiastical administration and a military presence
created conditions that encouraged the development of cities and towns. The theme system began slowly to be replaced by the emerging cities as centres of administrative, economic, and social life (Angold 1985: 7-9; Harvey 1989: 207; Dagron 2002; Bouras 2002: 501-4). There was a population increase and expansion of the urban inhabited area on the sites of the ancient agorai. Urban administration was carried on by the administration of the themata, and when the system declined, local powerful persons, the archontes, emerged as leaders of urban communities, together with bishops.
Then in a final phase:
In the eleventh century the cities again became centres of provincial administration with the krites (judge) as head of the civil administration of the theme. The large themes were subdivided into smaller ones and in reoccupied territories small administrative units were created in the district of each city: the Byzantine city was reaffirmed (Dagron 1987:160). [...] In the provinces the weakness of the central government during the eleventh century and at the end of the twelfth, together with fiscal oppression by imperial agents, created a discontent in the cities towards the capital marked by a sense of local solidarity. Local dynasts took power in provincial cities and led rebellions against the emperors.