From 1858 to 1869, St. John's owned Woodland Cottage, its first Rectory. The building is described as wooden Gothic Revival, located on Bay Street (then New York Avenue) diagonally opposite the present church structure. The first church building occupied the northwest corner of Belair Road and the lot adjacent to Woodland Cottage, This building still exists at 33-37 Belair Road, is landmarked, features an unusual stepped gable, tall facade windows, and an offset tower with a steep gable roof. It has a prominent centre chimney, casement windows with diamond-shaped panes and label mouldings, and a porch extending the width of the facade. The original structure was constructed by David Abbott Hayes, a lawyer from Newark, New Jersey, who sold it in 1849 to John Mayer, from whom the church purchased it. James Thompson, a Staten Island carpenter and builder acquired the house in 1869 and it remained in the possession of his heirs until 1948. Reportedly, the connection of Mr. Thompson with St. John's also included his role as carpenter for the exterior and interior carpentry of the church building completed in 1871, particularly noting the church doors and the entry porch. Mr. Thompson was also the builder of the parish hall or Mercer Memorial Chapel.
The Rev. Kingston Goddard was called to become rector, with a salary of $1,000 a year, $750 of which would be raised by pew rents, and the balance by private subscription. Dr. Goddard’s rectorship continued for three years, during which time the parish steadily increased in members and influence. He resigned in June 1847 to take charge of a church in Philadelphia.
The Rev. Dr. Alexander G. Mercer, a professor at the University of Pennsylvania, became rector on June 1, 1847 and remained until September 1852, when poor health caused him to resign. He was considered a “thinker and preacher of extraordinary powers, his manner so strong, so earnest, so full of dignity; he had the unconscious perfection of a work of art. His earnestness gave force and fire to the whole.”
The Rev. Richard M. Abercrombie, of Philadelphia, succeeded Dr. Mercer in January 1853 and served until February 1856. He led the parish in establishing a mission for the German population of the Island, built a chapel called St. Simon’s where a German version of the Book of Common Prayer was used, and a parochial school conducted. His devotedness to his office was valued by the church. He resigned to accept a large parish in Hartford, Connecticut on February 27, 1856.
On February 27, 1856 Rev. John C. Eccleston, D.D., was elected Rector and assumed charge of the parish on the 1st of April. It was his first ministerial assignment, having served an assistant in Lancaster, Pennsylvania. It was a time of intense materialism, suddenly changed by the Bank Panic of 1857. Banks suspended specie payments, businesses failed, railroads went bankrupt, construction halted, factories shut down. Hundreds of thousands of workers were laid off, and others went on part-time schedules or took wage cuts, just as the cold winter months were arriving. Where a general disinterest in religion had prevailed, a new focus on religion was formed, resulting in a Revival that increased church attendance. At St. John’s, constant services were held in the church during the Lenten season, and a class of nearly 100 persons was presented for confirmation.
At the end of 1862, Dr. Eccleston resigned to become rector of Trinity Church, Newark, New Jersey. The Rev. Dr. Thomas K. Conrad was called to fill the vacancy on January 1, 1863, and remained until October 1866. Dr. Eccleston became ill in January 1866 and resigned from the Newark church to take charge of a small church in Western Massachusetts. In the autumn of 1867 the vestry of St. John’s requested that he return, which he did on November 1, 1867, and remained for another 33 years.