Having heard the organ's principal chorus in the room, when the expression pedal was fully open, did it fill the room, yet not overpower?
If the volume of the pipework is incorrect on a pipe organ, revoicing may be required. Because of the complexity and expense of revoicing, you would need to work with other experienced organists, with institution leaders, and with your technician to solve this problem.
On an electronic organ, if you felt a need to close down the fully-open expression pedal for proper volume, or if you heard distortion in the speakers, the master volume or headphone volume may need adjustment. On some instruments the organist can make this adjustment, but on others a technician may be required. Follow the instructions in the manual.
When the headphones are plugged in, the headphone volume control can also be adjusted. See your instruction manual for specific directions.
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