St. John’s historic organ was originally designed and built in 1892 by James Cole and James Woodberry for the Highland Congregational Church in Lowell, Massachusetts.

When the building was demolished for freeway construction in 1970, the organ was disassembled and put into storage. In 1974, St. John’s Vestry purchased the organ, and the following April a "giant musical jigsaw puzzle" arrived in Kirkland by truck.

The organ consisted of about 10,000 pounds of pipes, chests, and boxes, which took a volunteer crew of 30 parishioners over five months to clean, reassemble, adjust, and tune.

The reassembled organ was dedicated at a recital that took place on October 6, 1974.