The 11th and 12th centuries saw three Popes from Montecassino: Pope Stefano IX, Pope Victor III (formerly the abbot Desiderius) and Pope Gelasius II. During this period Montecassino still experienced a beneficial yet independent relationship with the Papacy. However after the death of Oderisius I, in 1105, the abbey began to experience difficulty in terms of autonomy and leadership. While the abbot Desiderius had greatly influenced papal policy regarding cooperation with the conquering Normans, creating a policy of peace, Pope Honorius II (1124-1130) took on a rather different political strategy: one of ruthlessness and armed intervention. Montecassino, having enjoyed a history of sovereignty and independence suddenly found itself being coerced into answering to papal rule under Honorius II. The reversal of these previously cooperative policies in favor for anti-Norman policy, interference with abbot elections, dismissals and excommunications of Montecassino supporters and members (such as the young and influential Peter the Deacon, author of the Chronicle of Montecassino) all contributed to this era of instability.

After Pope Honorius II's death, the controversial double elections for the new Pope took place, creating a massively complicated schism, further dividing the peninsula and Europe. The 13th century was marked by continual stunted growth and difficulty due to the continual crisis in Europe, eventually starting to turn around in the 14th century with Pope Urban V who attempted to revive the historical hilltop abbey.