The majestic pipe organ of Espiritu Santo was completed in 1968 by Father Herman Schablitzki, SVD. It was Father Antonio Albrecht, SVD, who commissioned the work after he was assigned again as Parish priest of Espiritu Santo in 1958. Parts of the organ were imported from the factory of Laukhuff in Weikersheim, Germany.
It was said that the pipe organ was one of the best sounding organ in Manila presumably because of the great acoustic of the church. Repairs on the organ was made during the time of Monsignor Emmanuel Sunga during the 80's. The work was done by Marciano Jacela. Unfortunately, the condition of the organ was already in a bad state. It suffered during a minor earthquake in the 90's with some big pipes crushing onto the smaller pipes. When Diego Cera Organbuilders of Las Pinas took over the servicing of the organ in mid 90's. only 2/3 of the pipes were functioning. They tried to repair at least the horizontal trumpets and the chimes.
By the year 2002, problems on the pipe organ was just too much for the organist. Minor epairs will just be costly and would only be temporary. The choir transferred downstairs using an electronic organ.
The pipe organ finally got some hopes of sounding again by the year 2007 when Msgr. Alberto Salonga Jr. was appointed as Parish Priest. Plans were started for a complete Rehabilitation of the Pipe Organ. By January 31, 2009, a contract was signed between Msgr. Salonga and Cealwyn Tagle, head of Diego Cera Organbuilders for a complete overhaul of the pipe organ.