As with Angola, Portugal's hold on Mozambique at the time of the Congress of Berlin was precarious, and the Catholic presence minimal. In 1855 there were only four priests in the country (Helgesson 1991: 197).

Protestant missionaries from the 1870s went to the interior, still effectively under local chiefs. Protestants aimed especially at the south. The most significant influence was the Swiss Mission (Presbyterian) of the Free Church of Vaud, influenced by the reveil spirituality typical of much continental evangelicalism. The Mission formalised the Tsonga vernacular, generating a regional solidarity which became a taproot of nationalism (Birmingham 1992: 23). Cruz e Silva concludes that Presbyterianism helped the Tsonga resist Portuguese assimilationism; it also contributed indirectly to Mozambican nationalism through education, relatively democratic procedures and emphasis on Tsonga cultural values (1998: 236).

In addition, the Swiss Mission produced the founder of Frelimo, Eduardo Mondlane. Mondlane was educated by the Mission and worked as evangelist and mission school teacher. His studies in South Africa and the United States were paid for by Swiss Mission and Methodist scholarships, and there were hopes he might become general secretary of the Christian Council of Mozambique. Instead, Mondlane worked with the United Nations before founding Frelimo (Cruz e Silva 1998: 228–34; Helgesson 1994: 280). In Ngoenha's words, Mondlane converted his former Swiss Mission spiritual guides to his vision of a Mozambican identity, different both from the colonial idea of ‘black Portugueseness’ and the missionaries' idea of Tsongan-ness.