In March 1752, Schlatter returned to Philadelphia with the money and preachers, and in 1755 withdrew from his pastoral activities to become superintendent of the establishment of the schools among the Germans under the auspices of the Society for the Propagation of the Knowledge of God among the Germans, a group of people from London, of whom William Smith was secretary. The schools were unpopular with the Germans, and in 1757 Schlatter resigned his superintendency. He then accepted an offer by Lord Loudoun to become chaplain of the Royal American regiment, which he accompanied on an expedition to Louisburg. He remained with the army until 1759, and then preached at Chestnut Hill and surrounding places. In 1764 he was a chaplain to the 2nd Pennsylvania Battalion under Henry Bouquet on a mission against the Indians.