The Catholic Church arrived in the Kingdom of Kongo shortly after the first Portuguese explorers reached its shores in 1483. The Portuguese left several of their own number and kidnapped a group of Kongo including at least one nobleman, Kala ka Mfusu, taking them to Portugal where they stayed a year, learned Portuguese and were converted to Christianity. The group was returned to Kongo in 1485 and Kala ka Mfusu led a royal mission from Kongo's , Nzinga a Nkuwu to Portugal. Following their arrival in late 1486 the embassy stayed nearly four years in Lisbon with the monks of Saint John the Baptist. There they studied Christianity and Portuguese with Vicente dos Anjos (who also learned to speak Kikongo), and began the start of a Kongolese version of Christianity.

The mission returned to Kongo in early 1491, although Kala ka Mfusu died on the return trip. The provincial ruler of Soyo on the Atlantic coast received them and was the first to be baptized. They moved to the royal capital in April and May and Nzinga a Nkuwu was baptized on 3 May 1491, taking the name João in honor of the Portuguese king, (João II). Many of his officials and nobles were subsequently baptized. While initially reluctant to allow the baptism of women, his wife, Nzinga a Nlaza, protested and eventually won him over; she was subsequently baptized as Queen Leonor of Kongo and became a champion of the church, paying expenses from her own income.

Further missionaries arrived at the court of Nzinga a Nkuwu, beginning in 1508 and a good number also accompanied his son Afonso Mvemba a Nzinga to his provincial post of Nsundi. Afonso, in turn became a great champion of the faith, even though, according to Afonso's subsequent account of the events, his father cooled in the faith and many of the Kongolese who had been baptized turned away.

Reign of King Afonso

Afonso, whose letters are largely the sole source for the following events of his reign, presented himself to the world as a fervent Catholic, anxious to spread the faith, and also as having suffered persecution for it during the last years of his father's reign. When João died, probably in late 1506 or 1507, Afonso's half brother Mpanzu a Kitima, one of the lapsed Christians and a powerful rival, challenged the prince for the throne. But Afonso was able to overcome his brother in battle, thanks to having already positioned himself in the capital São Salvador and, according to Afonso's account the supernatural appearance of Saint James the Great in the sky, frightening his enemies. In subsequent correspondence with Portugal, Afonso decided to create a coat of arms in which five armed hands, each bearing a sword, was the principal element, along with a broken idol figured prominently. This coat of arms, first described in 1512, became one of Kongo's central icons, while Saint James Major's feast day became Kongo most important holiday, simultaneously honoring the saint who was popular in Iberian armies as a crusading saint, and King Afonso and his miracle.

Having become king, Afonso set about establishing a church. In letters to Portugal, he described some of the steps: he declared it illegal for people to worship idols, he destroyed a "house of idols" located in the capital (against the threat of a revolt), he also provided for a tithe to support it financially. Tradition from the late 17th century onward regarded Afonso as the founder of the church, and also attributes the story that he buried his own mother alive "for the sake of the Savior King" when she refused to take off a small idol she wore around her neck. Afonso's work to establish the church won him wide praise outside of Africa, and the Portuguese historian João de Barros called him the "Apostle of Congo" in 1552.

Afonso also worked to create a specifically local interpretation of Christianity, although the details are not well known. He worked with a number of Portuguese priests, most notably Rui d'Aguiar who came in 1516, and also with Kongolese who were educated in Europe, principally his son Henrique Kinu a Mvemba, who was elevated to the status of bishop in 1518, and who worked in Kongo from 1521 until his death in 1531.

Religious syncretism The Church that Afonso created was not simply a copy or extension of the Portuguese church, but from the very beginning included elements of Kongo theology. For example, the Kongos probably believed that most of the denizens of the Other World were the souls of deceased ancestors, and not gods who had never lived on earth or had a material existence. Thus, the catechism described the Holy Trinity as "three people" (). Priests were called by the same name as the previous clergy (), and the term , an abstract noun from the same root that gives the word (typically used to describe a charm, or in 16th century parlance, an "idol") was used to translate holy.

In fact, key religious terms such as God, holy, and spirit were rendered in Kikongo terms taken directly from Kongo cosmology ( for God, for holy and for spirit or soul). This in turn, made conversion easier, as self-identification requires only a simple declaration of faith.

In this way, the Bible was called which might also be rendered as "charm in the form of a book", and a church was called or "charm in the form of a building". In this way, Catholic saints were identified with local spiritual entities, and churches built in holy spots. This theology, developed by Afonso and a team of his colleagues, working with Portuguese priests, defined the way in which Kongolese approached the new religion and in many ways naturalized it.

Maturation of the Church Although Afonso is often credited with creating and establishing the church, it is probably his grandson and successor Diogo I Nkumbi a Mpudi who really placed the church on solid ground. Under Diogo, a lay organization of teachers first grew up to support and supplement the always meager number of ordained priests. Diogo also had the services of some of the earliest missionaries of the Jesuit Order, who worked in Kongo from 1548 to 1555. Diogo worked smoothly with the Jesuits when they first came, but as the Jesuits demanded more respect and worked at times against Diogo's political interests, he became disillusioned. Their mutually antagonistic correspondence with Portugal during this period has sometimes contributed to Diogo enjoying a reputation as a weak or uninterested Christian, though the events of his reign suggest that such a reputation was probably undeserved. Not only did Diogo arrange for the church to reach into the rural areas of the country, but he actively supported missionary work to the north (into the kingdom of Loango and south into Matamba, and he supported Jesuit work in Ndongo as well.

At the same time, as the church grew stronger, the King of Portugal decided to take greater control of it. He formalized his attempt to exercise control over Kongo's church by having the Pope place Kongo under the control of the newly created bishop of São Tomé in 1534. Many years elapsed between the formal subordination of Kongo to São Tomé and the first actual attempt of the bishop to exercise real control. When he did in the 1540, Diogo refused to allow the bishop to dismiss his personal confessor, Manuel Afonso. However, thanks to the mission of Antonio Vieira, a Kongo nobleman to Lisbon, and Duarte Lopes, a Portuguese representing Kongo visited Rome, the Pope granted Kongo its own bishop in 1596, with the church of Sao Salvador to be its cathedral. Portugal claimed the right of patronage over the new diocese, however and sought to use their control of the bishop to assert their own interests in Kongo, which were linked to the new Portuguese colony of Angola, founded in 1575. After many quarrels between the kings and bishops, in 1624 the bishop, moved, permanently, to Luanda and stopped ordaining new Kongo clergy.

Diogo and the kings that followed established a strong laity, into whose hands the job of education typically fell, while the small numbers of ordained clergy only performed the sacraments. This pattern, so visible in later Kongo history, was probably already present in the late 16th century. The lay ministers were typically designated as teachers (, in Portuguese), were drawn from the nobility of Kongo, paid salaries by the state, and engaged both in teaching literacy, religious education, and often also secretarial duties. The personal papers of Emanuele Ne Vunda reveal the workings of laymen's positions. When given charge of the church of the Trinity in Soyo, he was paid a portion of the fees that were paid for his services, including fees charged in burials. When he was made of the province of Mpemba, he was paid a salary of 6 of nzimbu shells a month, and also performed duties as a secretary.Antonio Manuel's papers are found in Archivio Segeto Vaticano, Miscellania, Armadio I, vol. 91 Collettione di Scritture di Spagna II, fols. 125 et seq. (One was equal to 10,000 shells.)

In 1604 King Álvaro II sent Ne Vunda as an ambassador to the Vatican. After travelling through Brazil and Spain he reached Rome on 3 January 1608, but died two days later of illness.

We have very little information about the numbers or lives of these though they were very important in the day-to-day life of the church. Their activities explain how the ordinary Kongolese managed to retain their version of Christianity even in the absence of ordained clergy. The certainly worked closely with the secular clergy of the country, and are often mentioned by the missionaries of the regular orders (primarily Jesuit and Capuchin) who visited and worked in Kongo in the seventeenth and eighteenth centuries.

Role of regular clergy The regular clergy (monks and teaching orders) had an important role to play in the development of Kongo's version of Christianity. Jesuit missionaries had a brief presence in 16th century Kongo (1548–1555), but political issues between them and King Diogo I brought the mission to an end.

A Discalced Carmelite mission worked in Kongo from 1584 to 1588 and Dominicans also had a brief mission in 1610–1612. However, it was the renewed Jesuit mission and the Capuchin mission that marked the real presence of regular orders in Kongo.

The Jesuits returned to Kongo in 1619, and in 1625 opened the college of São Salvador, which was responsible for the education of most of the Kongo elite in the mid 17th century. João de Paiva, the rector of the college until 1642, was particularly instrumental in the education of Kongolese, and also wrote an extensive, though now lost, chronicle of the country. Some of de Paiva's material informed the Synopsis Annalium of António Franco (1725). Jesuits also organized lay brotherhoods which played an important role in politics.

The Jesuits were followed in 1645 by the Capuchins. Capuchins came to Kongo largely because Kongo kings, beginning with Álvaro II of Kongo, were dissatisfied with the failure of the bishops to ordain sufficient clergy and the Portuguese crown's opposition to the ordination of Kongolese. Kongo demanded that its church be separated from that of Portugal and that Angolan interests from the rival and increasingly enemy colony that often controlled the episcopal office. As a compromise, the Papacy decided to send Italian Capuchins from areas that were not objectionable to Portugal to Kongo. Although officially missionaries, the Capuchins were as much like parish priests as missionaries to the unconverted. In fact, this parish priest role put them frequently at odds with the secular clergy, who Capuchins charged were lax in their duties and too tolerant of traditional Kongolese religion.