The album's liner notes state that "Pentecost III is dedicated to Tony Doyle, to Lin Mari Lowles, and to all the people who shared the grief of the terrible tragedy that befell us all this year 1994". Tony and Lin were two old friends of Anathema. Tony died from heart complications in his early twenties and, on the way to the funeral, Lin died in a traffic accident.
The track "Memento Mori" contains the hidden track "Nailed to the Cross/666". On the Pentecost III/Crestfallen EP re-issue this hidden track is moved to the end of "They Die", the last track on the disc.
The album artwork is a 1891 painting by Frederic Leighton called "Perseus and Andromeda".
Orchestral versions of "Kingdom" and "We, the Gods" were recorded for the 2011 compilation Falling Deeper.