The Menüçehr Mosque is most likely the first mosque built by the Seljuk Turks in Anatolia. This mosque, built at the edge of the gorge overlooking Arpa Çay (Akhurian River), is said to have been constructed by the emir called Manuchihr ibn Shavur. The Shaddadid dynasty, which ruled Ani from around the year 1072, began with him as the first ruler. However, the actual construction date and the origins of this structure are still stirring much controversy.

Some scholars, primarily of Armenian origin, assert that the structure predates the Turkish conquest, as it was initially a palace from the Bagratid era, subsequently transformed into a mosque. On the other hand, other scholars, mainly Turkish ones, maintain that the whole structure to be originally a mosque, erected just after the Turks conquered Ani. This would make the Menüçehr Mosque the earliest existing Turkish mosque in Anatolia. Finally, some other experts claim that even if the building was constructed as a mosque, it was in the later times, possibly in the 12th or 13th century as its architectural style suggests.

Actually, the oldest surviving part of the building is its intact minaret, standing at the northwest corner of the mosque. It has the Arabic word Bismillah ("In the name of God") in Kufic lettering high on its northern face. It most probably predates the present structure of the mosque, and was built on the octagonal plan. A steep spiral staircase leads anticlockwise around a central pillar to the top of the minaret. However, climbing the minaret is prohibited for safety reasons.

Interestingly, the building is not oriented in the normal direction for a mosque, facing Mecca, but it is about 20 degrees out. That would suggest that at least the foundations of an earlier structure were reused while it was built.

A rectangular building with dimensions of 18.5 by 15.7 meters, it represents an interesting combination of architectural styles: Armenian and Seljuk. It probably resulted from the Seljuks employing Armenian architects and stonemasons. A characteristic feature of the mosque are two-colour walls made of red and black stone.

The entrance to the mosque is at the northern end of the west façade. Inside, there is a rectangular prayer-hall with the roof originally supported by six columns. They divided the interior into eleven compartments, but currently only six of them exist. The hall was lit by five large windows.

Next to the mosque, there are the remains of a building that could have been a madrasa or a palace. Nearby there is also an area recently excavated by archaeologists, containing the remains of houses, a granary and baths.

In 1906, the mosque was partially repaired and another restoration of the building was initiated in June 2020.