The ancient Al-Aqsa Mosque remained closed until 1998, when it underwent restoration and preparation by the Heritage Committee and Al-Aqsa Foundation under Islamic endowments, allowing it to welcome worshippers again. It now has the capacity to host around a thousand worshippers at any given time. This section, known as the lower mosque, is located beneath the southern mosque and was built during the Umayyad period.

Architecturally, the mosque features distinctive elements such as two flat Umayyad domes that sit above its southern entrance, supported by massive stone columns that also serve as the foundation for the area of the Dome of the Qibli Mosque. Access to this prayer area is via a stone staircase situated near the middle colonnade on the northern side of the Qibli Mosque.

The renewed visibility and access to the ancient mosque not only highlights its religious significance but also its cultural heritage, reflecting a blend of history and spirituality that resonates with both local and international communities. The efforts to restore and maintain the ancient Al-Aqsa Mosque are crucial for preserving its identity and functionality within the Islamic tradition, while also serving as a site of immense historical importance.