History of Europe

Christinanity and Islam.
There really is no good answer to this question. There were a number of pairs of religions that fought in Europe during the Middle Ages.

If you need a simple answer, the wars involving followers of Christianity and Islam are the more significant to historians. Nevertheless, wars between Christians and Pagans possibly involved more people and certainly extended over a longer time.

In the Early Middle Ages, wars between Christians and Pagans happened in what had been the West Roman Empire. They soon stopped there, but continued in central, northern, and eastern Europe. We might include Viking incursions into the rest of Europe in these. These wars in the North and East continued into the High Middle Ages, and were still going on after the last Crusades to the Holy Land.

Wars between Christians and Muslims happened in both the East and West. The wars in the East began as Muslims conquered much of what remained of the East Roman Empire, but they did not really arrive in Europe for some time after that, and were mostly confined to the Balkans. In the West, a different set of wars centered on Muslims who invaded territories that are now in Spain, Portugal, and France.