By the late 1800s, the cemetery was a casualty of San Diego's expansion. In 1889, a streetcar line was built directly through the cemetery, bisecting the plot. The brick chapel built by the Workman family was destroyed in a fire. In 1917, Walter Temple, a grandson of the Workmans, sued to prevent further destruction to the cemetery, and had a new mausoleum built to replace the family chapel lost to fire.
More damage was to come, however. In 1942, parts of the cemetery were paved over in the construction of San Diego Avenue. The number of graves which have been paved over is unknown, although some have been identified through the use of ground-penetrating radar. A bronze plaque on the cemetery wall acknowledges that graves were lost to city expansion, and along the sidewalk, there are occasional bronze circles stating simply, Grave Site.
Perhaps understandably, El Campo Santo is reported to be the site of paranormal activity, particularly on San Diego Avenue. Over the years, people who parked on the street (and unwittingly on someone's grave) have reported cars that won't start and horns blaring for no reason. There have also been sightings of the spirit of a young woman just outside the cemetery gates.
El Campo Santo was added to the National Register of Historic Places in November of 1974.