No matter, it's fairly certain Oakland will not tender Alvarez a contract entering his final year of arbitration eligibility after signing him to a one-year deal last winter.
Andrews performed Alvarez's first surgery in July 2015 to repair a tear in his shoulder.
"I feel really bad for the guy based on the fact he worked so hard to get back," manager Bob Melvin said. "He's such a great guy, loves to pitch, each and every time he was on the verge of pitching, he couldn't wait, and then to be disappointed in that fashion every time, certainly you feel for him.
"Now that he has to have surgery again, that's not ideal, but at least he knows what's going on in there now and fixing it will be the next step in getting him back pitching again."
A's head trainer Nick Paparesta said Andrews will perform the surgery in Pensacola, Fla., and wouldn't speculate on a timetable for his rehab.
"They found some things they thought need to be addressed and handled, and they're going to be able to address them once they get into surgery," Paparesta said, "but the extent of them, I won't know until they're done."
Alvarez logged 33 innings in 11 Minor League rehab starts this season, but suffered setbacks on three occasions, each as he was nearing a return.
Alvarez is just 26 years old, but he faces an uphill climb back to a Major League mound, considering the complexities of shoulder injuries. Alvarez was an All-Star in 2014 with the Marlins, going 12-7 with a 2.65 ERA.
Jane Lee has covered the A's for MLB.com since 2010. Follow her on Twitter @JaneMLB. This story was not subject to the approval of Major League Baseball or its clubs.