The Old Protestant Cemetery was founded in 1821 after the British East India Company purchased a plot of land to address a need for Protestants to be buried within the Catholic Portuguese colony of Macau. Robert Morrison, who is buried here, was instrumental in lobbying for the cemetery's purchase. Prior to 1821, Protestants had to bury their dead secretly in the no-man's-land between Macau and China, neither of which was willing to allow such burials in their territories. A number of graves were relocated from outside the Macau walls into the cemetery. The cemetery accepted burials until 1858, when another cemetery, the New Protestant Cemetery, was opened.

In the 1970s and 1980s, the British academics Lindsay and May Ride conducted a great deal of research on the history of the cemetery and those buried there, publishing their findings in a book entitled "An East India Company Cemetery: Protestant Burials in Macao". They also founded an organization to take care of the cemetery, which is now well tended and in excellent condition.

The cemetery grounds consist of three terraced levels. Just within the gates, near the Camoes Grotto and Gardens, is the Morrison Chapel, which contains two memorial plaques. The next terrace down contains around 45 graves, and the remaining graves are in the lowest and largest terrace. Set in the wall separating the lower terraces are 23 old headstones that were found stacked in the New Protestant Cemetery, having been moved there perhaps a century before. The bodies buried under those headstones, which had been outside the city walls, are long lost, and as such these should be considered cenotaphs. The one exception is that of Lindsay Ride, whose ashes are buried in the cemetery.