The land around the current location of the cemetery has been used as a burial ground beginning in the mid to late 18th century, with the earliest above-ground markers associated with Pensacola's Second Spanish Period.

After officially being designated a cemetery by King Charles IV of Spain in 1807, it was moved to the south and east, and was formally platted out by Vincente Pintado in 1810.

Although originally designated for Catholic inhabitants, the cemetery has traditionally served as a burial ground for people of all faiths.

As Pensacola has drawn immigrants from around the world, it is the resting place of Captains of Industry, victims of Yellow Fever epidemics and steam ship explosions, along with those who died in child birth, as infants, and of old age.

Today the cemetery has about 3,200 marked graves, excluding many unmarked graves, and is primarily maintained by St. Michael's Cemetery Foundation of Pensacola, Inc., a non-profit organization working with the University of West Florida.