The physical facilities of the Foundation consist of a three story building the size of a triple car garage located on Mercer Island, Washington. On the bottom level is the storage area where organs are brought before they are rebuilt. There is space on this level to store a complete organ of moderate size as well as a number of additional pipe organ parts.

On the second level is the Foundation shop with the tools necessary to rebuild consoles, windchests, pipes, and other organ parts.

On the top level is the organ assembly room where parts of the organ being rebuilt are put together. A chain hoist is used to bring large items such as consoles and windchests up from the shop level to the assembly room.