Even though the organ was much improved as a result of these changes, it was still operated with the help of a human "organ blower." Stain glass windows were probably installed at ' this time.

Until about 1830, the Frederick Presbyterians had no regularly installed pastors, , but had preaching services conducted by supplies who stayed for a few months or for several years, usually working with other small churches in the Monocacy Valley. One of the first pastors, the Rev. Patrick Davidson (1810-1824), was also principal of the Frederick Academy. For nearly fifty years the pastors of the Church also served as principals of the Frederick Academy, an honored boys’ preparatory school now out of existence. The Rev. Dr. Knox, a part-time pastor of the church, was the founder of the Frederick Academy. With the arrival of Rev. James Hamner in 1830, the congregation began to keep more systematic records and to establish their distinctive role in the community.

The year of 1830 also marked the establishment of the Sabbath School as distinctly Presbyterian. Up to this time the children of the church had been instructed in a school conducted by the Episcopalians and the Presbyterians in common.

Rev. John B. Ross, M.D., was installed as pastor of the church on November 1, 1857. Shortly thereafter, the Civil War began to affect Maryland, a border state. According to the historian/pastor, the Rev. Thomas Freeman Dixon, "Troublesome times came, especially for those who dwelt along the border line, house was divided against house, brother against brother, and father against son." The Church was no exception, for both the Union and the Confederates sides had their friends and supporters. During these troubled years, Rev. Ross was visited by his personal Presbyterian friend, General Stonewall Jackson, and in 1862 the tree to which Jackson tethered his horse was known as the "Stonewall Jackson Tree" for years to come. In 1862, the work of pastoring became so difficult and discouraging for Dr. Ross that he gave it up.

For nearly two years the church was without a pastor and part of the time the church was used as a hospital for wounded soldiers, especially after the battle of Antietam. Another time Dr. Dixon wrote, “This is not the only association which this building has had with the war, for during nearby cannonading a ball fell through the roof and hung in the ceiling just above the pulpit, from this position of peril to the pastor the ball was removed and sold at a fabulous price to a gentleman who took it to California, and for a long time the mark remained as a silent witness of the ruthlessness of the war." Jacob Engelbrecht, a local resident who kept an extensive diary, noted on July 6, 1864, of the artillery shell that is said to have pierced the church roof. The repairs to the roof and ceiling were made in 1868.

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