He returned to Connecticut in 1723, under the auspices of the Society for the Propagation of the Gospel in Foreign Parts, as a missionary priest. He opened the first Anglican church built in the colony, Christ Church, Stratford, Connecticut in 1724. In 1725, Johnson, the son of a fulling miller, married the widow Charity Floyd Nicoll, the mother of three young children, one of whom, William Nicoll, was heir to the vast estate of Islip Grange, in Sayville, New York, then part of a 100 square mile estate on Long Island owned by the Matthias Nicoll family. Johnson thus acquired close contacts with the leading merchant, legal, and political families of New York colony, many of whom would send their sons to board with him in Stratford, to be prepared for college. His first son by Charity, William Samuel Johnson, was born on October 14, 1727; his second son, William "Billy" Johnson, was born on March 9, 1731.