In 1553, Wallachian voivode Pătrașcu the Good and his son Ioan Vodă cel Cumplit cracked down on the village spreading havoc; in 1600, Habsburg general Basta raided Csíkszék; but the deadliest attack came in 1661, when the Tartars set the church, monastery and the school on fire destroying them.

Among the founders of the grammar school was Johannes Caioni (1629–1687), who was an architect, composer, organ builder and player, historian, and printer.

Even Basta, the cruel Habsburg general donated wealth, and during his raids, he managed to avoid causing damage to the monks here.

The largest donations were from Hungarian Gabriel Bethlen in 1616, George I Rákóczi, in 1649, Ákos Barcsay in 1659, and Michael I Apafi in 1662.

Csíksomlyó became a pilgrimage site in 1567, when Hungarian king John II Sigismund Zápolya wanted to convert the Székely population of the upper Csík to Protestantism.

The monks saw this as a sign of the care of Virgin Mary, and since then, this event has been commemorated by a pilgrimage when the believers gather on Pentecost every year.

Beside its religious importance, the pilgrimage has also become a community event demonstrating spiritual unity of Hungarian people living in and outside the historical region of Transylvania.