The non-profit Spreckels Organ Society was founded in 1988 to preserve and program this unique civic asset located in the heart of Balboa Park. The Spreckels Organ Society welcomes members, who receive the quarterly StopTab newsletter along with invitations to special events. Members are entitled to a discount on all purchases at the Spreckels Organ Gift Shop (at the Organ Pavilion during concerts). Funds from membership and donations support organ programming, a scholarship program for student organists, Family Festival Day outreach to young audiences, and guest artists who perform with the Spreckels Organ.

While expanded and improved over the years, the organ utilizes the same innovative electro-pneumatic design originated by the builder, the Austin Organ Company of Hartford, Connecticut. Now maintained by co-curators Lyle Blackinton and Dale Sorenson of L.W. Blackinton & Associates, the organ is capable of performing the full range of organ repertoire from classical to theatre organ styles.

The Spreckels Organ Pavilion was built in 1914 specifically to house the Spreckels Organ and was designed by Harrison Albright, whose work for the Spreckels companies included the Spreckels Theatre, the U.S. Grant Hotel, the Spreckels mansion in Coronado, and other buildings. Today the Pavilion is administered by the San Diego Park & Recreation Department, which offers permits to use the facility for events that are free and open to the public. Among the popular events staged annually at the Spreckels Organ Pavilion are the annual Community Christmas Center, the Easter Sunrise Service, the summertime Twilight in the Park musical series, all planned by a variety of community organizations.

Concerts on the Spreckels Organ are overseen by only the eighth person in history to have held the position of San Diego Civic Organist, Raúl Prieto Ramírez.

Prieto Ramírez was Artistic Director and Founder of the Barcelona Summer Organ Festival and Academy, where he attracted audiences by the thousands. His joy is making great music exciting and accessible for everyone – especially kids – and he is well known for being one of the few concert organists who performs from memory. His powerful personality, passionate expressiveness, gift for communication, and outstanding technique make him shine in a wide range of repertoire and styles. Critics have praised his performances at major venues all over the world as "simply awe-inspiring," "electrifying," "colossally talented," "fearless," and "audience rose to its feet with applause at every opportunity."