1000 CE, the relationship among Christians and Jews was quite amicable. Likewise, during this timeframe, Christians and Muslims maintained a mutually beneficial existence. As the Middle Ages progressed, Christians began to exert more control over the non-universal practices and beliefs adhered to by their religious and political leaders. Christianity faced the Great Schism when the Catholic Church in the West and the Eastern Orthodox Church separated.

By the time of the First Crusade around 1096 CE, the Church faced still another dilemma. The Church had become more militaristic and challenged the Muslim World. The Jews were barred from participating in the Crusades since their religion forbade them to bear arms. This strained the Christian-Jewish relationship.

The Christian response to these challenges that arose after the fall of Rome was to embrace universal religious beliefs while forming a new way of life for the remaining Empire. Under the old Roman rule, the citizenry focused on health, exercise, baths, extravaganzas, wealth, and material things. Romans were obsessed with laws more than worship. They loved to travel, and their culture was steeped in entertainment. The new Christians cared little about many of the old Roman obsessions. They were more interested in their souls than their bodies. They embraced poverty where it existed and believed it was akin to godliness. Thus, in the early days of the Middle Ages, the Church remained poor, although this would change drastically centuries later.

Christians between 500 CE and 1000 CE adopted the belief that the greatest human pleasure was to praise God and the simple life of worship was the means to peace and happiness. This, however, rapidly changed. The new Christianity faced some major difficulties. First, the Christian economy deteriorated into communities of near abject poverty. Second, the people required protection from the growing number of enemies threatening their survival. Third, Christian religious beliefs began to conflict with science.

The Christian response was the greater centralization of power in the Pope to the extent that governments in Western Europe were ruled by the will of the Pope with the blessing of their political leaders. Additionally, the rise of monasticism helped to organize and unify Christian doctrine throughout Europe through the spread of monasteries. It was not long before the papacy and the monasteries themselves grew very wealthy through the widespread support of their followers. Additionally, religious zeal enabled Christian leaders to amass armies to ensure profitable trade and other commerce. Ultimately, the Crusades accomplished very little except to cement the idea of theocratic governance into Western Europe. The conflict with the scientific world continued long thereafter.

The Early and High Middle Ages were formative times for the Catholic Church. The fall of the Western Roman Empire in the late fifth century set the Church on a path that would see it as one of the few uniting forces in the region. Catholic leaders were presented with numerous barbarian peoples, some of whom were more receptive to Christianity than others. Missionary efforts led to the conversion of the Visigoths, Lombards, Franks, Anglo-Saxons, Vikings, and others. As a common faith among so many different and sometimes antagonistic peoples, the Catholic Church often found itself in the difficult spot of picking sides and being the peacemaker.

In the seventh century, the Byzantine prohibition of icons led to a major rift. This and several other ecclesiastical differences saw the Eastern Orthodox Church and the Catholic Churches take separate paths. At times, they would come to each other's aid. Other times, they acted more as antagonists. When Charlemagne invested the office of the Pope with the title Patricius Romanorum in 800, the Catholic Church became fully independent from Constantinople. Over the next two and a half centuries, the Eastern and Western churches maintained a strained relationship that culminated in a complete schism in 1054.

The partnership between the Catholic Church and secular leaders led to some challenges. For instance, the power to appoint members of the clergy became a recurring bone of contention. This led to the Investiture controversy of the eleventh and twelfth centuries. In short, this was a struggle between the Church and the Holy Roman Emperor over who had the power to appoint high-ranking clergy, including the Pope himself.

The latter half of the eleventh century saw an effort to rid the Church of corruption. Known as the Gregorian Reforms, initiated by Pope Gregory VII, these efforts reaffirmed papal authority and attacked practices of simony and clerical marriage.