With the founding of the DAI's Baghdad Department in 1955, German archaeological research active in Iraq since 1887 became institutionalised in its host country. The department was to carry on with research, which earlier on  had already reached much public acclaim under the projects led by the German Oriental Society (Deutsche Orient-Gesellschaft, DOG) in Babylon, Assur, and Uruk between 1898 and 1917, and those in Uruk between 1928 and 1939. The founding director of the Baghdad Department, Heinrich Lenzen, continued above all with the excavations in Uruk-Warka whilst concentrating on the architecture of the Late Uruk Period. This was supplemented by follow-up investigations in Babylon, where in 1962 work began on its famously known tower, the Etemenanki ziggurrat. Moreover, architectural surveys were carried out at the Abbasid Madrasa al-Mustansiriya in Baghdad, one of the few earlier Islamic buildings to have survived the centuries (1227 AD). Brief investigations in the Sasanian capital Ctesiphon, surveys in the Iraqi desert region west of the Euphrates, excavations at Tulul al-Ukhaidir, and research on rock monuments from Assyrian and Parthian times in Northern Iraq completed the programme. In cooperation with the Iraqi antiquities administration, settlements from the Kassite Period were uncovered in 1978/79 as part of rescue excavations carried out in the Hamrin area.

Owing to the political developments in Iraq as from the Gulf wars in 1980–1988 and 1990–91, the trade embargo 1990–2003, the invasion in 2003 and the civil war-like conflicts until 2011, the work of the Baghdad branch office received a more  culture-political orientation. Regular research stays in Iraq have again become possible since 2011, at first in the Kurdistan Federal Region, and since 2015 also in Southern Iraq.

In 1996, the Baghdad Department was attributed the status of a branch office of the newly founded Orient Department.