Mention of Holy Trinity Church has been found as early as 1163. At that time it was located closer to the cathedral. The present building dates (in parts) from around 1412. John Knox preached here with considerable vigor, inciting crowds to ransack the cathedral in 1559. An unlikely legend says that the pulpit from which Knox preached is now located in St. Salvator's Chapel. Above the Iona marble pulpit hangs the battalion standard of the 2nd Fifeshire Militia, which was formed in St. Andrews at the time of a threatened invasion by Napoleon.

In 1800 the church was greatly altered from it's 1412 design, but it was restored again in 1909 to much of its former (1412) layout.

Even today the church is indeed a museum of St. Andrews' history, containing such artifacts as the relatively benign "penitant stools" to the more macbre instruments called "branks" used to silence the tongues of those found guilty of gossip or blasphemy. Archbishop Sharp is said to have ordered their use on a woman who opposed his preaching in 1673.

An original wooden pew bearing the royal coat of arms of Mary Queen of Scots is still in the church.

The church tower was at one time also used as a prison.

Archbishop Sharp's Tomb, with translation from Latin of the inscription. The tomb was comissioned by his son Sir William Sharp, was constructed of Greek and Italian marble in Holland, and placed in the church in the same year as his murder ... 1679

On the east wall of the south aisle is the marble tomb of Archbishop James Sharp, murdered by Covenanters on Magus Muir in 1679. When the tomb was opened in 1849 there was no trace of Sharp's bones. What became of them nobody knows though one theory is that the presbyterian kirk session could not stand the idea of an Episcopal bishop lying in state in the church and gave some sort of cooperation to whoever bore off the relics.