In 1887, the sum of $332.00 was expended for improvements of the Church and parsonage property, the windows of the Church having been crushed by a hail storm.

In his "History of the Jersey Shore Methodist Church", Dr. Emery M. Stevens, one of the former pastors, gives a memorable account of the famous June flood of 1889. Dr. Stevens reached the field on April 4th, and found the parsonage in the midst of repairs, paint and carpets. On the evening of May 30th it began to rain, continuing for 48 hours. The flood in the West Branch Valley was without precedent, and millions of dollars of damage was done. The pastor, accompanied by his family, had gone to Salladasburg on the 30th to address a memorial meeting at night; the rain kept him there on the 31st, and his family did not reach home for two weeks. The water stood two feet, eight inches in the parsonage. Kind friends and neighbors had taken up the best carpets; everything else went afloat. The fences and buildings in the lot were destroyed. But the greatest damage was done in the Church building. The water was six feet eight inches in the Sunday School room. The floor came up, stove, organ and library were destroyed, many of the benches were broken, windows damaged, wainscoting torn down and frescoing peeled off to be replaced by one of mud. The damage on Church and parsonage property was not less than $1,000.00. The Church Extension Society sent the congregation $100 toward repairs, and this was further increased by $250 given by the church-at-large through the "Christian Advocate". A total of about $500, all the money on hand, was expended to repair and refurnish the Sunday School room so the school could use it during the winter. During the summer of 1890, the repairs were completed. The Trustees then proposed that the audience room, which was in a rather dilapidated condition, should be made equally beautiful with the Sunday School room. The majority of the congregation thought that this was not possible. The Audience room was frescoed in new designs, wood work finished in mahogany, pulpit platform lowered, choir gallery built and carpet laid, making the Church on both floors probably the most beautiful of its size in the Williamsport District. The total cost of these repairs, in addition to amount expended in the fall of 1889, was $1300, all of which was provided for before reopening day. The reopening service was October 26, 1890.

In 1896, the Rev. Edward E. Mulliner, the father of Miss Mary Mulliner, was licensed to preach the Gospel. From that date until his death in 1918, he continued as the local preacher of First Church.

In 1897 extensive repairs were made again. The presiding Elder's report for that year says, "Jersey Shore has so completely transformed the Church building inside and outside that former pastors would hardly know it. The audience room is one of the most pleasant and inviting to be found in the District, and best of all, there is no debt."