Abstract Hagia Sophia’s hypogeum is a group of subterranean Roman tomb structures located in the area between the northeastern side of the structure and the imaret (“soup kitchen”) of Hagia Sophia. Consisting of three chambers connected by a passage, the hypogeum is dated to the fourth century and older than the current Hagia Sophia. The story of the architectural documentation of the hypogeum is also interesting. As a matter of fact, exposed findings during the museum research still contribute to the dating studies of the structure. The first digital architectural visualisation of the space was made in 2020 within the documentation of the subterranean structures of Hagia Sophia. After the partial cleaning of the inner space at the end of 2021, a relatively more favourable environment allowed for its visualisation. This study presents the most recent architectural documentation of the hypogeum carried out, the first reconstruction plan proposal, and a virtual superposition of the structure with its superstructure. Completely cleaning the interior and top will enable this space to be thoroughly documented and dated. By including the narrative of the documentation story to the present, this study is expected to be the last visualisation of the hypogeum until it is completely cleaned. The lack of architecturally similar structures in Istanbul requires special attention to this subterranean structure.