Many Centre presidents also were Presbyterian pastors, and, at the time of the Battle of Perryville, Centre President Lewis Warner Green regularly took the pulpit. Green initially was connected to Danville's Second Presbyterian, but when that church burned in the February 1860 fire, the First Presbyterian Church opened its doors to that congregation. Thus, two ministers shared pastoral duties during much of the Civil War.
Fox later described the church as "a very fine structure." In 1862, the building contained a large sanctuary with a gallery, or balcony, on three sides, each supported by brick pillars. The pews could seat more than 700 people, and they were, Fox noted, "finished in natural finish and varnish." The interior also included "very nice pulpit furniture" that Danville resident G.W. Welsh, who was a Centre student in 1862 (and was later a cashier for Farmers National Bank) described as "a high pulpit, with four or five steps up to it, with a railing around it on two sides, and running around part of the way in front." The church was carpeted, all of the walls were plastered, and an unfinished basement contained storage space for coal and wood.
Sick and wounded Union soldiers occupied the Presbyterian Church immediately after the Battle of Perryville. Welsh, the Centre student, saw the Federal soldiers in the church every day as he walked to his classes. Pews placed together served as beds for the troops, and, one resident remarked, the sick "occupied both the auditorium and the gallery."
Danville resident W.W. Tompkins, a house painter and plasterer after the Civil War, knew firsthand what these injured soldiers were experiencing. During the war, Tompkins was a member of Company A of the Fourth Kentucky Infantry Regiment. The regiment was organized by Danville native and Union General Speed Smith Fry. These soldiers took part in the Perryville campaign but did not fight in the battle. After Perryville, Tompkins' regiment pursued the Confederates toward Crab Orchard. Here, Tompkins fell ill, was given leave, and went home to Danville, where he stayed until January 1863.
Tompkins later explained, "During that time I visited these different churches that were occupied by the forces of the United States Army. I done that for the reason that I was hunting some comrades that were sick or wounded. The Presbyterian Church was one of the churches that I visited." During these excursions he discovered that the Presbyterian Church was nearly completely filled with wounded and the sick.
Occupied until the spring of 1863, the building was left in shambles. Stoves were destroyed, the pulpit was gone (presumably smashed and burned for firewood), windows were broken, many pews were removed and destroyed, walls were scribbled upon, and plaster was damaged.
Danville resident Patty Engleman later described the scene. "The pews had been used as beds for the soldiers," she said, "Names were cut on them, and they were cut in various ways. The side walls were knocked in places, like a hammer had been taken and knocked against them. They were pecked in a great many places. The pulpit was very much defaced. ... It was cut and scratched. It was in such a condition you would not want it for a church. ... The carpet was ruined. It was all gone; it was in rags, not a remnant of it was left."