St. Johns owns three pianos: a Baldwin grand in Loring Hall, a Yamaha upright in the choir room, and an early 20th-century restored Steinway model B in the sanctuary. A single-manual Flemish-style harpsichord is on loan, as is a Steinway model A grand piano.

A two-octave set of Whitechapel English handbells belongs to the church. The set was completely refurbished in 2018. The bells were polished, and all mechanical parts tuned up.

​In the Sanctuary is a three-manual, 48-stop M.P. Moller and Sons. organ, installed in 1964, which includes a separate 81-note keyboard mounted on a simple stand with music rack and four controls for stops. Cables are installed between this auxiliary keyboard and the Positiv division. There is an installation by the Solid State Organ System Company, installed in 2006. It includes the MultiSystem with MIDI capability and a MultiLevel Capture Combination System with 64 levels.

The stop list is to the left.

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