Esphigmenou ranks eighteenth in the hierarchy of the Athonite monasteries and since the early 1970s has been embroiled in legal and ecclesiastical disputes.

However, historical and archaeological evidence cannot safely confirm this tradition and, therefore, the precise time of the monastery's foundation, as well as its founders, cannot be positively identified.

However, the monastery managed to recover eventually, as evidenced by a manuscript dated from 1569 that tells of 51 monks working for its reestablishment.

In 1655, Czar Alexis I of Russia gave the monks permission to travel throughout his lands every five years to raise funds for the monastery.

A series of competent abbots (Acacius, Euthymius, Theodoritus, and Agathangellus) greatly renovated and expanded the monastery, to the point where the current structures date almost exclusively from their time.

During the Greek War of Independence, the monastery, being the northernmost on the peninsula, suffered gravely from the Ottoman armies that ravaged Mount Athos.

[5] Since the Constitution of Greece prohibits schismatics (or Roman Catholics) from dwelling in Athos, the occupants of Esphigmenou were ordered by a Thessaloniki court to leave the monastery; however they refused to comply.

In November 2005 Katsoulieris and his monks tried to take over the ‘old’ Esphigmenou konaki in Karyes (building 23), but failed and the police had to be invoked to separate the parties.

[6] Esphigmenou again gained global attention in December 2006 when members of the new brotherhood tried to force their way into the monastery's offices in Karyes (in the "old" konaki at nr 23).

[7] In January 2007, the district attorney of Thessaloniki pressed charges against the monks of Esphigmenou ("σχισματικοί ρασοφόροι") for "embezzlement" of over 150,000 euros and the estate rightfully belonging to the monastery.

[9] The monks continued to remain inside the premises of Esphigmenou Monastery, under blockade, as shown in a 2016 travel documentary by British presenter Simon Reeve.

In January 2017, eight monks of 'old' Esphigmenou monastic community, including abbot Methodios (Papalamprakopoulos), received jail sentences in-absentia from Thessaloniki Mixed Jury Criminal Court.

The monks were charged with instigating violence and throwing Molotov cocktails at police officers following an incident in July 2013 in the Athonite capital of Karyes (relating to the occupation of the 'old' konaki building).

The incident in question occurred when court bailiffs arrived to the Esphigmenou administrative offices in Karyes on July 29, 2013, to evict the schismatic monks, who responded by throwing three Molotov cocktails and an explosive device.

[10] In April 2019, the monks inhabiting the buildings of Esphigmenou Monastery, considered squatters by the Ecumenical Patriarchate and the Sacred Community of Mt.

[11] A few days later, a Thessaloniki appeals court handed down a sentence of 17-years’ imprisonment and a fine of 600 euros for the abbot Methodios and the monk Antypas for the 2013 attacks.

On July 23 police officers arrived at the monastery's dependencies in Ierissos and in Nea Roda and forced the monks to leave.

The iconostasis in particular, which depicts scenes from the Old and the New Testaments, is carved wood, covered with golden plating and is considered one of the most important post-Byzantine iconostases on Athos.

The catholicon also has two chapels, a vestibule and a porch, added in 1845 by Ecumenical Patriarch Anthimus VI of Constantinople, a previous Esphigmenite monk.

Its iconography, dating back to the 16th and 17th centuries still survives, albeit greatly damaged by the fires that the Ottoman soldiers lit to accommodate themselves during their stay in the monastery during the Greek revolutionary war.

Of the outer chapels, the most notable is the chapel of Saint Anthony of Kiev, the founder of the Kiev Pechersk Lavra — St. Anthony's life states he became a monk on Athos and Esphigmenou's tradition has his having lived in a secluded cave there overlooking the sea, which is still shown to visitors, and he is commemorated on the feast for All Saints of Esphigmenou — that lies just across from the monastery.

Among important cultural treasures, such as crosses, books, garments, etc., Esphigmenou has in its possession a large (3.05×2.80 m) part of Napoleon Bonaparte's tent, which was donated to the monastery by Patriarch Gregory V of Constantinople.

The so-called Cross of Pulcheria lies at the catholicon's altar, which also houses cases of holy relics and a very important Byzantine mosaic icon.

The library also holds a collection of roughly 2,000 printed books, while 6,000 more are housed in another part of the monastery, on the second floor of the northern wing.