[2] The initial board of trustees consisted of Abraham H. Van Wyck, Caleb S. Woodwell, C. Edwards Lester, Charles Miller, Luther R. Marsh, Edwin Williams, and Christian Delavan.

[6] In 1902, during the construction of the Interboro Parkway through Cypress Hills, charges were laid of gross mismanagement by trustees who re-elected themselves each year without oversight, and who received a large income from the sale of burial plots but did not spend any of this on improvements to the cemetery.

Scandal erupted in 1998 when it was revealed that a section of the cemetery was built on unstable landfill; the cemetery had constructed the Terrace Meadow hill on landfill as a way to increase burial space and appeal to customers who sought burial plots on a hill with a good view.

The New York State Supreme Court ruled that the area was unstable and all graves had to be moved.

[8] In 2003, charges were laid by Ravi Batra, one of its former court-appointed guardians, who accused another of trying to seize control by quietly installing one of his own employees as president of the cemetery's re-formed board of directors in a bid to gain control of the 200-acre (0.81 km2) cemetery.