It is built on top of a rock near the sea near the middle of the eastern shore of the Athonite Peninsula, located between the monasteries of Iviron and Pantokratoros.

In 1533, The monks of Philotheou sold Stavronikita to the abbot of a Thesprotian monastery, Gregorios Giromeriatis (Greek: Γρηγόριος Γηρομερειάτης).

During the Greek War of Independence in the early 19th century, Stavronikita, as well as the whole of Mount Athos, experienced harsh times.

The monastery faced a harsh economic situation due to extraordinary debt that helped fund the war, while its monks were scattered after the Ottomans invaded Athos.

This situation lasted for about a decade, after which the Ottomans left Athos and any monks that had survived started returning to the monastery.

Important sights of the monastery are its characteristics, the tower at the entrance, its aqueduct, as well as its centuries old cypress outside the western corner of the complex.

The catholicon is decorated with frescoes and an iconostasis by the famous icon-painter Theophanes of Crete and his son Symeon.

The monastery's refectory is located on the upper floor at the southern side of the complex and bears some important iconographies.

The rock was found to be slowly crumbling and sliding towards the sea which led to concerns about the future of the monastery's structural stability.

), a state organization under the jurisdiction of the Ministry for Macedonia–Thrace, undertook the task of renovating and restoring the monastery.

Extensive renovating work took place from 1981 to 1999 and by applying a complex engineering method the underlying rock was stabilized.