The monastery takes its name from the landscape it inhabits — and that name, Varnakova, is almost certainly pre-Greek in origin, a Slavic toponym left over from the migrations of the early medieval centuries. The founder, Saint Arsenius the Varnakovite, established the community here in 1077 during the mid-Byzantine period. Why this particular hillside, on the southwestern edge of Phocis, overlooking the mountainous country of Nafpaktia and Doris with views toward Mount Giona and the Mornos river valley? The sources don't say. But the logic is familiar from dozens of Byzantine monastic foundations: a place of water, forest, altitude, and some quality of seclusion that the founders found right. The dense forest of oak and horse chestnut that surrounds it today was almost certainly already there in the 11th century.

The Ottoman centuries were hard on most institutions of Greek Orthodox life, but Varnakova survived — as a keeper of manuscripts, of ecclesiastical tradition, and eventually of armed resistance. During the Greek War of Independence, which began in 1821, the monasteries of the mountains above the gulf played roles that went well beyond the spiritual. Varnakova became one of the places where the struggle for Greek independence was sheltered and sustained in the rugged terrain of Roumeli. The monastery's own publications describe these years in terms of heroism and sacrifice; its title, the Holy Lavra of Roumeli, echoes the role of the Lavra of Agia Lavra near Kalavryta on the Peloponnese, where the bishop Germanos is traditionally said to have raised the standard of revolt in March 1821. The comparison the monks draw is not modest, but it reflects a genuine regional memory of the institution as something more than a place of worship.

For centuries, the monastery's most venerated object was its icon of the Panagia Varnakova — the Virgin as she appears in the iconographic tradition of Byzantine Orthodoxy. The icon bore a distinctive physical mark: an obvious crack running across the face of the Virgin. According to eyewitnesses, the crack appeared during a local earthquake on August 15, 1940. That date is also the Feast of the Dormition of the Theotokos, one of the most important days in the Orthodox calendar. The coincidence of the earthquake with that feast day, and with another event that had just occurred hundreds of kilometers away — the torpedoing of the Greek cruiser Elli by an Italian submarine in the harbor of Tinos — gave the crack the character of a sign in local memory. The icon was displayed with the crack visible, the fracture itself becoming part of what was venerated. On June 14, 2020, fire destroyed the icon, along with other historical relics of the monastery.

The monastery stands on a small hill on the outskirts of the Vardousia Mountains, approximately 25 kilometers northeast of Nafpaktos by the old road of Lidoriki. Its setting is one of the things visitors remark on first. The dense forest presses close — oak and chestnut — and through the trees, on clear days, the views open south toward mountainous Nafpaktia and east toward the limestone massifs of Doris and Mount Giona. The Mornos river, which drains much of this mountain country, is visible below. That combination of enclosure and prospect — forest intimacy giving way to enormous sky and mountain — gives Varnakova a quality of contemplative geography rare even among Greek monasteries, which tend to choose their landscapes well.