The majority of the Muslim and Croat population was expelled, or departed the city, during the war in Bosnia, while the town saw a massive influx of Serbian refugees from the surrounding Bosniak-held areas, and from cities far away as Sarajevo. This effectively changed the area's demographic creating ethinically monolitical areas dominated by Serbs in the Republika Srpska, and mainly Bosniaks in the neighboring Federation municipalities. At the outset of the Bosnian war the city was taken by the Serbs; it was heavily shelled by Bosniak and Croat forces throughout the conflict causing numerous civilian casualties, especially during the latter half of 1995.

Croat-populated parts of the pre-war Doboj municipality and the municipality of Tesanj, both of which have been in the Federation since 1992, were consolidated into the Municipality of Usora. Usora, a historic local toponym, is also a suburb of Doboj and the nearby river.

It is relevant to note that figures above pertain to the pre-war municipality of which parts are in the Federation of Bosnia and Herzegovina, and are predominantly Bosniak (namely the Federation municipalities of Doboj East and Doboj South which are over 95% Bosniak, and Usora, which is Croat), which reduces the figures pertaining to the number of Bosniaks and Croats in the territory of the municipality within the boundaries of the Republika Srpska (to around 25 thousand Bosniaks and around 9 thousand Croats).

Doboj saw the overwhelming Bosniak return (around 15,000 in 2001, according to the UNHCR figures) to the municipal area in the RS as well as the near perfect completion of the process of property reposessions. In addition, the numbers have increased further since 2001. These processes were implemented by the UNHCR, OSCE and the Office of the High Representative in cooperation with municipal authorities. Many Bosniaks returned to town, while many Serb displaced persons remained in it as well. Doboj ranks among the most multi ethnic cities in the entire country, sharply contrasting its entire wider region.