This church, which was perhaps part of an ancient monastery, is believed to have been founded by John the Short, who lived at Wadi al-Natrun and also founded a monastery there. He fled that area in 407 AD after raiders had made the region unsafe. However, the current church may date back to about the end of the 5th Century.  

The Church of Abu Hinnis is interesting from an architectural standpoint, and has attracted considerable attention because it shows most clearly the changes that were made from a church with a basilican plan to one roofed with domes and obstructed by clumsy masses of brickwork to support them. Originally, the church probably had a only one sanctuary with an apse and two small rooms on either side. 

Today it consists of a narthex (entry vestibule), a nave and two sanctuaries at the rear of the church. The nave is divided into three bays, and covered by three domes. The piers that support the domes are so large that they completely block the interior, leaving it with little light. The three bays of the nave consist of a southern part known as a gynaikion, or women's chamber, a central area reserved for men, while the eastern bay is for the choir. 

There are two sanctuaries, or haikals, with one dedicated to the Holy Virgin (northern) while the other is dedicated to Saint John the Short (southern). In the north sanctuary dedicated to the Holy Virgin, there is an icon depicting Saint John the Short, which is a 19th century relic provided as a gift by Demetrius, the 111th patriarch of Alexandria. Another icon depicts Macarius.In the sanctuary dedicated to Saint John the Short, there is a 17th century icon depicting the Holy Virgin, and an icon dated to 1837 that portrays Saint John the Short. There is also a Greek Jerusalem proskynitarion from the 19th Century, which is a so8uvenir picture that provided orthodox pilgrims with most of the important religious sites and commemorations in the Holy Land. Proskynitarions were produced by Greek artists in Jerusalem. 

West of the northern sanctuary of the Holy Virgin is the baptistery. The semi-circular apse (altar) walls are ornamented with three niches. Here, and along both longitudinal walls where there are three more niches, are located twenty columns with acanthus-leaf capitals and temple fragments used in the construction of this church that once were parts of much older antiquities.

There are other interesting Christian antiquities in the area near this church. The ancient Coptic Orthodox Church had two types of monks, including anchorites, or hermits, and cenobites who lived in a monastic community. However, sometimes hermits lived in the same general area and formed what was called a laura. These hermits prayed, ate and worked alone in their caves, which generally consisted of only one room for living and working and one room for sleeping and prayer. They only met with other brothers during the Divine Liturgy in church.

East of the village of Deir Abu Hinnis in the mountains are the remains of a 6th century laura consisting of at least 37 caves extending over a distance of more than two kilometers. Many of these caves are adorned with Christian graffiti. There is also a church hewn from rock of probably two or three ancient caves which may go back to the earliest Christian centuries (though it more likely dating to the 6th or 7th centuries AD). According to some authorities, this may be the martyrion (martyry, "martyr-church") of Saint Colluthus. 

This church, today known as the Cave Church of Saint John the Short, has a western entrance narthex that is unusually large. It is approached by a flight of steps from above. 

The walls of this church are covered with ancient paintings, though unfortunately, most are only dim reminders of its ancient decorations. Most of the faces of people within the paintings have been purposely destroyed. However, these wall paintings, all of the same style and apparently dating to the 6th or 7th century, have attracted considerable attention from archaeologists. 

After entering the church, the room to the right includes paintings depicting he Massacre of the Innocents, with King Herod sitting on his throne in the temple and assisting in the massacre. The end of the wall is adorned with representations of Zachariah and Elizabeth, which may belong to the Massacre of the Innocents. Other scenes portray the Apparition of the Angle Gabriel to Saint Joseph, and the Flight into Egypt of the Holy Virgin and the baby Jesus on an ass, together with Saint Joseph. Within a niche are wall paintings depicting five individuals, including Christ and the Holy Virgin at the wedding at Cana, where Christ changed the water into wine with a rod. 

The room opposite this to the left is adorned with wall paintings of the Resurrection of Lazarus. Other paintings portray the life of Zachariah with the angel Gabriel in the temple.  There are also numerous Coptic inscriptions on the walls of the church. 

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