As the pope of the largest and oldest Christian community in the Middle East, Shenouda III belonged to a Coptic tradition that can be traced back to when St Mark introduced Christianity to Egypt in the 1st century AD. The first decade of his tenure, which began in 1971, was characterised by fierce protest and dissent against the government, mainly over its failure to protect Copts from attacks by Muslim extremists. As a result, Shenouda was expelled from his post by President Anwar Sadat for four years. Following Sadat's assassination and Shenouda's return to Cairo, he became a model of co-operation with the government for the rest of his life.

Shenouda III's ambition was to find a place for the Coptic population within Egypt in a country where 90 per cent of the population are Muslims. He attempted to smooth over some of the problems that resulted in attacks against Christians in the early 1970s by appealing to the name of "one God whom we all worship", although renewed deadly attacks by Muslim extremists on the Christian Coptic community in more recent years showed that this strategy was having limited success. He also gave explicit support to the Palestinians in their conflict and developed good relations with a number of Muslim religious leaders to the extent that he was dubbed "the Arabs' pope".

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