Because of its exceptional value to national history, the Archdiocesan Archives in Zagreb is organizationally subordinated to the Department of the Croatian State Archives in Zagreb. It began operating immediately after the Zagreb Diocese was established in 1094. Due to the date of its establishment, it is the oldest archive in the inland part of Croatia. Namely, in 1914, the Zagreb Archdiocese concluded an agreement with the Royal Croatian-Slavonian-Dalmatian Government on the terms of storage of the records in the Royal Territorial Archives for fifty years. The same agreement stipulated that the Metropolitan Library of the Archdiocese of Zagreb would also be deposited at the then Royal University Library. Today, the Croatian State Archives has the Zagreb Archdiocese Department, which consists of two parts: the Archdiocesan Archives and the Metropolitan Library. At the beginning of the 1980s, the archival materials were relocated from the then National Archives of Croatia on Marulić square 21 to the addresses Kaptol 27 and 31, where the Archdiocesan Archives are today, while the Metropolitan Library remained at the same address. Besides  the documentation of the archdiocese, the archives also hold the materials of various associations related to the Zagreb Archdiocese, then of archbishops, auxiliary bishops, deacons, parishes and personal archives of many laypersons.

The oldest document in the archives is Felician's Charter from 1134. Likewise, the archives contain abundant materials on the relationship between the Zagreb Church and the Universal Church, as well as the political, economic and cultural role of the Zagreb Church and its bishops. The most important sort of archival materials were taken by Bishop Maksimilijan Vrhovac at the turn of the 18^th into the 19^th century. Namely, historian and archivist Martin J. Kovačić and his son Josip N. Kovačić divided the archbishop's archives of the time into ten thematic categories, including theory, privileges, tithes, economic writings, court records, ecclesiastical writings, ecclesiastical administration documents, founding documents and expropriation documents. Likewise, both of them also processed the correspondence of Zagreb bishops in the period from 1611 to 1815. The archives have great importance to the history of the Zagreb Archdiocese, but also northern Croatia in general. it is certainly of great importance are The canonical visitations of the Zagreb bishops and the scriptures of Zagreb bishops from the 12^th to 20^th centuries certainly have great importance, as do the writings of archdeacons about political, religious and cultural circumstances in the territory of the Zagreb Archdiocese from 1615 to the most recent times.