As a Christian man, at this time, we find him teaching a large Bible-class for young men in the above church, and to the end of his earthly career he was constantly engaged in the Sabbath-school.
In 1849 the Prince Street Church property was sold to erect a new building on Twelfth Street, where he continued to attend the services until the year 1850, when some of the members, being anxious to enlarge their borders, and continue the work in the lower part of the city, formed the Second Reformed Presbyterian Church. They organized, and called the Rev. Spencer L. Finney to the pastorate, who commenced to hold services in the hall of the Apprentices' Library, No. 472 Broadway, where they worshipped for one year, and then secured more ample accommodations in which to worship God, in the rooms of the Medical College, Crosby Street, near Spring.
In 1850 he was carefully examined, and when found qualified for the sacred office, was duly ordained a ruling elder in the Second Reformed Presbyterian Church.
During the year 1854 the Church purchased the building in Mulberry Street, near Grand, belonging to the Lutheran body.
At this time he continued to reside on the west side of the city, and attended two sessions of the Sabbath-school morning and afternoon, with two preaching services, and one prayer-meeting in the evening.
As soon as the congregation were permanently settled in a church building, he removed from the west to the east side of the city, to the Tenth Ward, in order to be in close proximity to his church work.
He continued to worship with the Second Reformed Presbyterian Church, under the pastorate of the Rev. S. L. Finney, who, in 1863, was called to Princeton, N.J.
The Rev. Geo. S. Chambers was subsequently called to take the pastoral charge. Eventually, it was found essential to change their ecclesiastical relations from the Reformed Presbyterian Church to the Old School, from which time (the two religious bodies having become united), the congregation became known as the Ebenezer Presbyterian Church.
In due course it united with the Fortieth Street Presbyterian Church, afterward called the Murray Hill Presbyterian Church, because at the time, though in possession of a church building, they had no pastor. Mr. Knowles continued to attend regularly until the imperative demands of age and time called for change, when he became united with the Allen Street Church.
In 1870 he accepted an invitation from his uncle to visit his native place; and he frequently afterward remarked that the scenes of his boyhood's days had materially changed as much as he had; realizing that change, progress, and decay were written upon all things terrestrial.