In 1143, during the Crusades, King Foulques and Queen Melisende purchased the village of Bethany from the Patriarch of the Holy Sepulchre in exchange for land near Hebron. Melisende built a large Benedictine convent dedicated to Mary and Martha, extensively repaired the 600 year old church of St. Lazarus, and rededicated it to Mary and Martha.

The abbey of Ss Mary and Martha was separated from the tomb of Lazarus by a small cave cut from the rock. Pilgrims entered the site, as today, from the north side. From the court in which they found themselves, they could then have turned east to enter the church of Sts Mary and Martha, or west to enter the crypt-chapel which gave access to the tomb of Lazarus.

"The buildings of the medieval convent are known to extend some 45 meters south from the walls of the two churches and at least 57 meters from east to west.... Enough of the complex survives...to suggest that a functional distinction was observed between the western or upper part, which seems to have contained the conventual buildings of the nuns, and the lower eastern part which was given over to store-rooms and kitchens. The finest architectural detailing to survive anywhere in the convent...appears to have represented the eastern portico of a cloister...lying immediately south of the west of the church." [The Churches of the Crusader Kingdom of Jerusalem: A Corpus: Volume 1]

After the fall of the Crusader kingdom in 1187, the nuns went into exile. The church was probably destroyed at this time, with only the tomb and barrel vaulting surviving; the 6th-century church and tower were heavily damaged but remained standing.

By 1384, a mosque had been built on the site. In the 16th century, the Mosque of al-Uzair (Ezra) was built in the Crusader vault, which initially made Christian access to the tomb more difficult. However, the Franciscans were permitted to cut a new entrance on the north side of the tomb and at some point, the original entrance from the mosque was blocked.

From 1952-55, a modern Franciscan church dedicated to St. Lazarus was built over the Byzantine church of St. Lazarus and Crusader church of Ss Mary and Martha. In 1965, a Greek church was built just west of the Tomb of Lazarus.

The forecourt of the Franciscan Church of St. Lazarus stands over the west end of the older churches, from which parts of the original mosaic floor are preserved. The west wall of the forecourt contains the west facade of the 6th-century basilica, with three doorways. The cruciform-plan church stands over the east end of the older churches. Trapdoors in the floor just inside reveal parts of the apse of the 4th-century church (the Lazarium), which was shorter than the 6th-century church. The modern church bears a mosaic on its facade depicting Mary, Martha and Lazarus. The interior is decorated with polished stone and mosaics.

Just up the hill on the left is the 16th-century Mosque of al-Uzair. The courtyard is in the Byzantine church atrium and the mosque is built in the vault that formerly supported the west end of the 12th-century church. A further 25meters up the hill on the left is the modern entrance to the Tomb of Lazarus, which is accessed by 24 very uneven stone steps. This probably was a rock-cut tomb, but very little of its original form remains. The rock probably collapsed under the weight of the large Crusader church built above it.

The original blocked entrance can be seen in the east wall of the antechamber; this alignment suggests the tomb predates the Byzantine churches and may well be from the time of Lazarus. Even further up the hill is a modern Greek Orthodox church that incorporates a wall of the Crusader church built over the tomb.