Documents and images are not mere testimonies of the past, but more importantly repositories of knowledge able to serve as correctives in history of science and as a resource for new approaches in academic research. The Istanbul Department is in charge of four separately managed archives: the department archives, the photo archive, the Pergamon archive, and the Boğazköy archive. They store, index, and impart files, bequests, as well as the institute's excavation and survey records and research projects. The archives, especially the photo archive, are of outstanding importance for Turkish research and monument preservation in Istanbul and hence of priceless value for knowledge acquisition.

The creation of the department's archive began in 2011. Its main components are files from the directorate, bequests from renowned scholars and building researchers, and also excavation records. Most of the archive is stored in two archive rooms specially prepared for this purpose in 2012. The shares dating to the pre-war and war periods (1924-1944, and sporadic records dating back to 1887) were made accessible for research in 2013. As far as established, this partial collection is fully preserved. Its 127 directory items comprise the official correspondence of Martin Schede from his time as head of the branch office of the Staatliche Museen zu Berlin in Constantinople (1924-1929) and subsequently of the DAI-Abteilung Konstantinopel, renamed to Abteilung Istanbul in 1930.

Among the records dating to the period after the war are for instance the (partial) bequests of some important scholars like Ernest Mamboury, Alfons Maria Schneider, and Wolfgang Müller-Wiener.

Furthermore, the Istanbul Department houses a photo archive (see photo archive), the Pergamon archive, and the archive of the excavations at Boğazköy. The documents stored in the excavation archives continue to serve as important sources for research of the respective excavation sites. Parts of the excavation archives are located at the DAI headquarters in Berlin. These are kept separately and merely are managed by the department archive in Istanbul. Owing to Pergamon's long and eventful excavation history, the archives of the Pergamon archive are spread over five locations other than Istanbul. They consist chiefly of older documents dating back to 1878, and next to Istanbul are kept in Berlin (DAI headquarters; SMB Antikensammlung), Munich (DAI-AEK), Bergama (DAI excavation house), and Athens (DAI-Dept.).

The digitisation and free accessibility of archived documents is an important part of the work at the archives. Digital copies are created by aid of the archiving software AtoM and are not only accessible in the online iDAI.archives, but also clearly identified as to their physical storage location.