Morley last visited Yucatán and the Hacienda Chenku in spring of 1948, just months before his death. He escorted a party to the ruins of Uxmal in February, on what was possibly his last visit to a Maya ruin. He died in Santa Fe on September 2, 1948, aged 65, two years after the publication of "The Ancient Maya". He was buried in a plot in Santa Fe's Fairview Cemetery; his second wife Frances Rhoads Morley was interred in the same plot upon her death in 1955.