In March 1863 Admiral David D. Porter and General Leonard F. Ross led the Yazoo Pass Expedition against Confederate-held Fort Pemberton. After the expedition had departed, Quinby’s division was sent out as reinforcements. Quinby met Ross and Porter on March 20 and learned the expedition had failed but convinced them to return and try again. The continuation resulted in two more unsuccessful artillery duels and the expedition ended for good on April 5. During the expedition Quinby became ill and took a leave of absence and General Marcellus M. Crocker assumed command of the 7th Division. Having recovered, Quinby returned to duty on the morning of May 16 but it was deemed necessary for General Crocker to retain command of the division as they were deploying for Battle at Champion Hill. Quinby agreed, concluding he was still in a feeble condition from the journey to rejoin the army. He did however remain on the field until the battle was decided only then did he officially assume command of the division. Quinby led his division during the May 22 assaults on Vicksburg. During the siege, on June 3, Quinby’s health began to fail him again and went on another sick leave, only this time he would not return to field command. He returned to New York where he commanded a Draft Depot at Elmira, New York before he resigned from the army on December 31, 1863.