Burials here dated from November 19, 1791 (SCZ Death 00001) through December 19, 1850 (SCZ Death 02177). The cemetery may have been used until the establishment of "Old Holy Cross Cemetery" in 1873, but there are no burial records for the period 1851-1873. In 1885, many remains, most unidentified, were transferred to "Old Holy Cross Cemetery" where they were re-interred in a mass grave.
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The original Mission Santa Cruz cemetery lay to the east of the old mission's adobe church and was irregularly shaped. It extended east from the front (southeast) corner of the church to a point where it angled to the north east. At a point about 150 feet east, a wall angled west to the church almost parallel with the front or southern cemetery wall. Comparing the 1854 Black survey with a plot map of Fallon's land east of the cemetery surveyed by T. W. Wright in 1851, it appears that the northern portion of the west line of Fallon's lot corresponds to the southern portion of the eastern cemetery wall. Fallon's rear or northern boundary line appears as an extension of the east-west cemetery wall.

The Black survey shows a line (possibly a wall), shot to the northeast corner of the eastern wing of the quadrangle. Judging from the topography, it would appear that this area north and rear of the cemetery lie down the hillside northeast of the church. This area may have been used as a burial ground when the older original part was full. In any case, burials were discovered in the area northeast of the church in 1950 when the area was graded and they are shown in photographs of the 1920s era. This observation is born out by newspaper references (Santa Cruz Sentinel, September 2, 1885; Santa Cruz Daily Surf, September 16, 1889). Discrepancies exist between the Fallon survey of 1851, the Black survey of 1854 and the Surveyor General's survey by John Wallace in 1858, concerning the length of the old adobe cemetery wall running from the survey post south to a point at right angles to the front of the church. Scaling from the Fallon map it was 150 feet long; from Black, 125 feet long, and from Wallace, 132 feet long. The latter puts the rear line at 138.6 feet at a scale of 20 chains/inch.

Most importantly, the Wallace (Deputy U. S. Surveyor General) map of 1858 shows the old adobe church in relation to the new wood church of 1858, discussed below. At this point in time, very little of the old church, other than the facade itself, had fallen or been cleared away, it appears. It is important to note that the facade of the new wood church of 1858 was shown with the facade absolutely aligned with that of the old adobe church. Also, a vestige of the adobe bell tower and front buttress was shown still in place on the southeast side of the adobe church facade.

Eventually, a new brick church was proposed for the site of the old mission church. Because the new church was to be substantially wider than the mission church (about 25 feet), it was necessary to excavate the graveyard west of the church. An announcement was published in the Daily Surf, July 23, 1885: "The old cemetery will be leveled to the grade of the rest of the ground and those who desire will remove the remains of friends buried there. Others will remain under the new church, which however, will cover only a portion of the ground devoted to the cemetery."

(Kimbro, Edna E. "Construction Chronology of the Site of Holy Cross Church: Ex-Mission Santa Cruz became Holy Cross", Santa Cruz Public Library)