The history of the Presbyterian Church of Mozambique goes back  to 1882 when Josefa Mhalamhala was sent to preach the gospel in present-day Mozambique by the Church of Valdezia/Spelonken in South Africa, belonging to the Swiss Mission. Rev. Paul Berthoud, the first missionary sent by the Swiss Mission arrived in 1887. Ricatla, where today the theological seminary is located, was the first mission station. In 1948 the church assumed its own financial responsibilities. At a meeting of representatives of the church and the Swiss Mission in 1962 the autonomy of the church was officially recognized, and the status of the missionaries serving the church was clarified. An important synod of the church was held in 1963, in Lourenço Marques (now Maputo), where a new constitution was adopted and five pastors were ordained. In 1970 autonomy became a reality when all mission stations became the property of the church. The Portuguese government was not happy to see these changes. Between 1972-74 the church suffered greatly at the hands of the colonial authorities. Many Presbyterian church leaders were imprisoned in 1972. The president of the synod council, Rev. Zedequias Manganhlea and one of the elders were killed in the infamous Machava concentration camp.

The Presbyterian Church of Mozambique is growing. Before independence it was working in only two provinces of the southern part of Mozambique. At that time Protestantism was mostly concentrated in the south, the centre was more Catholic and the north more Muslim. Now the church is preaching the gospel in all ten provinces and the number of Christians is increasing. Other independent churches and some new churches like the Universal Church of the Kingdom of God are also moving from the south to the north.

Evangelization has always been accompanied by the social work of the Presbyterian Church, for example, hospitals, schools, etc. The church has had a profound influence on the cultural, social and political life of the people. The founder of the Liberation Front of Mozambique, Edouard Chivambo Mondlane was a member of this church, as is the newly-elected president of the country. The Presbyterian Church of Mozambique continues to search for new forms of Christian presence within society by equipping its community with a mature, biblical faith. The training of the laity and the education of youth through various programmes are priorities on the agenda of the church.