During the first four years of its existence, the settlement, which has been estimated at about 270 persons, did not have an ordained clergyman. The first one, Jonas Michel, who arrived on April 7, 1628, was of French descent. Following the custom of Dutch clergy at the time, he latinized his name to Jonas Michaelius. He began conducting regular services in a room above the village's grist mill on what is now William Street near Pearl Street. It seems he spoke French rather well and that he could preach in French after a fashion. It is certain that he began holding regular French services every Sunday afternoon following the morning service in Dutch. The date chosen for the founding of the French Church of Saint-Esprit is somewhat symbolic. In a letter dated August 11, 1628, Michaelius wrote to a colleague in Amsterdam that "the Lord's Supper was administered to them (the French and Walloons) in the French language, and according to the French mode with a discourse proceeding, which I had before me in writing, as I could not trust myself extemporaneously." Easter Day, 1628, thus became the date chosen to represent the founding of Saint-Esprit.

Jonas Michaelius returned to Holland in 1633. For the next fifty years the religious needs of the French-speaking population were met as well as possible by the various Dutch clergymen. From comprising almost a majority in the beginning, the French-speaking segment of New Amsterdam (New York after 1664) declined steadily, although it never entirely disappeared. The first wave of persecution against the French Protestants during the time of the St. Bartholomew's Day Massacre was finally resolved by the Promulgation of the Edict of Nantes in 1598 which gave legal status to the Reformed religion. The influx of new refugees stopped. Following a pattern that was to be repeated in the future, the Huguenots who migrated to other lands worked hard, prospered, quickly intermarried with the residents of their new country, and lost their comfort with the French language.

The second and largest influx of Protestant arrivals from France began in the last quarter of the 17th century. Louis XIV renewed the persecution of Protestants in a series of harsh repressive measures which culminated in the Revocation of the Edict of Nantes in 1685 and the determined effort not only to crush all practice of the Reformed religion in France but to forcibly convert all Protestants to Catholicism. This tragic and misguided action drove from France hundreds of thousands of her most able and industrious people. It enriched those countries and colonies who, wisely, offered them shelter. England was the place of refuge for Huguenots from the maritime provinces of western France: Poitou, Saintonge, anad Aunis. A smaller number came from the rest of France, especially Normandy. From England, thousands migrated to the colonies in America. Jean Maynard, in his history of Saint-Esprit, estimates that the French Church of New York received about one-quarter of one percent of the overall Huguenot immigration. This percentage was enough, however, to dramatically increase the French-speaking population of New York. By 1697, according to Dr. Maynard, there were 4,000 inhabitants of New York City and, of that number, about 15 percent were Huguenots.

The first independent French Church was organized under the Rev. Pierre Daille who had been a professor at the French Protestant college of Saumur before it was closed by order of the king and its faculty banished. Seeking refuge in Holland, Mr. Daille then went to London where he received Anglican holy orders. He came to America to work with the French and Dutch, not only in Manhattan, but in the surrounding area, going on a regular schedule to Huguenot communities in New Paltz, Staten Island, and New Jersey.

In 1687 he was aided by the arrival of the Rev. Pierre Peiret, a native of Languedoc in the South of France. Concentrating on the French of New York while Mr. Daille continued his work in the surrounding area, Mr. Peiret organized the first French congregation to have its own edifice. This small church was located on what was then called Petticoat Lane, later Marketfield Street. Today it is Battery Place between Broadway and West Streets. It was called simply "L'Eglise Francaise a la Nouvelle York."