On June 23, 2012, after a save against the New York Yankees, Francisco was placed on the 15-day disabled list after feeling soreness in his oblique muscle. Before he began a rehabilitation assignment to come off the DL, Francisco aggravated his injury. On August 22, 2012, Francisco showed frustration by hurling a cooler in the dugout after giving up two runs in the top of the ninth inning. On December 18, 2012, Francisco had surgery to remove a bone spur from his right elbow.