Continuing his work with the Provincial Congress, John Pigeon was elected to serve as commissary of stores on February 22, 1775. On May 19, 1775, the position of commissary general was created, and Pigeon became the first appointee to act "as a commissary for the army of this colony." Records show that Pigeon was overwhelmed with the role, as he offered to resign by the following month. At his request, a committee was appointed to assist with the work, and he requested both deputy commissaries and additional supervisors to the main camps. By July 1775, the Continental Congress took over the army and appointed a new commissary general for the entire army. Though out of the role as commissary general, the detailed records he left in his ledger are credited by researchers for helping document new information on the Siege of Boston.