After attending the gymnasium of his native city, Michael received theological training under the private tuition of Prof. Casper Wegelin of St. Gall and at the universities of Leyden in Holland and Helmstedt in Germany.
On April 10, 1739, Schlatter was examined for the ministry and ordained. For a while he was a private tutor in Holland, but in 1744 he became vicar to John Jacob Beyel, Dekan of Wigoldingen, Thurgau, Switzerland, and, a year later, Sunday evening preacher in a suburb of St. Gall.
In January 1746 he left St. Gall for Heidelberg, where he met Prof. Johan Caspar Cruciger, one of the leading men of the Reformed church of the Palatinate, who directed his attention to the needs of the Reformed churches of Pennsylvania. As a result, Schlatter offered his services to the Synods of Holland, under whose auspices the missionary work was carried on.
He was commissioned for service in Pennsylvania on May 23, 1746, and arrived at his post in September 1746, beginning at once a strenuous and many-sided missionary activity. His first efforts were directed towards organizing the Reformed churches of Pennsylvania into a synod under the supervision of the Reformed Church of Holland.
His next task was to organize the widely-scattered Reformed congregations into regular pastoral charges. He made a series of extensive missionary tours throughout Pennsylvania, Maryland, Virginia, and New Jersey, and found forty-six congregations which he organized into sixteen pastoral charges. There were, however, only four ordained Reformed ministers in the province, so he returned to Holland, in February 1751, in order to secure more pastors.
His appeal, printed in Dutch in 1751 and in German in 1752, was so successful that he not only gained the consent of the Holland synods for a larger number of missionaries in Pennsylvania, but was also able to interest the states of Holland and West Friesland in his work, so that they voted a subsidy of fl. 2, 000 annually for a period of five years for his work. With this financial backing Schlatter went to Germany where he secured six young men, who accompanied him to Pennsylvania.
After his return he turned his attention to the education of the children of the new settlers. He found few church schools, poorly equipped, and very unsatisfactory teachers. In the interests of this cause he returned once more to Holland in November 1753.
In June 1754 the Synods of Holland released him from their employ so that he might accept the position of superintendent of schools in Pennsylvania under an appointment by an English society, which had been formed to carry on this educational work. The project was conducted in Pennsylvania by a body of general trustees, of whom William Smith was the secretary.
In the fall of 1754, six so-called "charity schools" were opened, the number later being increased to nine. But this undertaking failed because the local Germans were antagonized by the political motives of the English society, and Schlatter retired in 1756.
Later he entered the British army as chaplain. On March 25, 1757, John Campbell Loudoun appointed him as one of the chaplains of the Royal American Regiment and he took part in the siege of Halifax, the capture of Louisbourg, and in the expedition to capture Fort Duquesne.
Schlatter returned to Philadelphia in October 1759 and assumed the pastorate of several independent Reformed churches, notably Barren Hill, near Philadelphia. When Henry Bouquet organized an expedition to destroy the Indian forts on the banks of the Muskingum in 1764, Schlatter was commissioned as chaplain of the 2nd Pennsylvania Battalion and thus held a chaplain's commission both under the British and the provincial authorities.
He died in Philadelphia.
Schlatter was married to Maria Henrica Schleidorn, daughter of Henry Schleidorn of New York City. They had nine children, one son and five daughters surviving their parents.