The latest update to the Clipper transit payment system was supposed to make things easier for travelers in the Bay Area, by consolidating transfers and allowing for credit card tapping. But so far, the rollout has been plagued by operational problems that are making some people so upset they’re venting on social media.
The Clipper system serves BART, AC Transit, and 22 other Bay Area transit systems, with more than 1.2 million cards in use in December 2025, the last month for which Clipper data is available. The highest number of unique Clipper cards used in a month in recent years was 1.37 million in June 2025.
Since the Clipper Card upgrade rolled out on Dec. 10, users have been reporting problems. Some people have said they’ve been unable to access the digital cash balance they had before the upgrade; others have said their cards became inoperable or they had difficulty adding money to them.
Kerry McDaniel told Richmondside by email that a BART staffer verified their $40 deposit on Dec. 8 but it then disappeared. After inquiring several times, they still had no answers and the money remains missing.
“Clipper support said that I need to contact them by phone. But when I tried, the wait was usually at least 40 minutes, so I hung up each time. It’s also not clear to me that this will help,” McDaniel said. “Is it the responsibility of each person who lost their deposit to phone for a correction, and can they actually get help that way? Or is this something that will, and should, be corrected by some overall software correction at some future time? I simply don’t know. In the grand scheme of things $40 is not a lot. I can let it go, if I have to. The real issue is the sheer confusion.”
John Goodwin, a press officer for the Metropolitan Transportation Commission, acknowledged a raft of card issues and said Clipper engineers have been working to fix them. The MTC manages the Clipper Card program through a vendor, Concord-based Cubic Transportation Systems.
Goodwin said that there are several “buckets” of issues the agency and Cubic Transportation are facing but insisted that “many of the issues customers have encountered appear to be either unique or limited to small groups of customers.”
A critical one is poor system performance. Goodwin said that Cubic’s customer relationship management system (CRM), has experienced several outages since the update, making it impossible for some people to access their accounts via the Clipper mobile app or website. The Clipper call center, where customers can turn for help, has also gone down intermittently.
“Cubic continues to investigate and is working on fixes to CRM data queries and its server configuration,” Goodwin said.
Another key issue, he said, is malfunctioning card vending machines and terminals.
He said San Francisco riders have reported performance issues with Muni ticket machines to the agency. Goodwin said that the Muni machines are expected to receive a software update that should fix these problems soon.
Botched card migration
More than half a million Clipper cards have been migrated to the new system, Goodwin has said, but Cubic is still doing extensive manual cleanup of card data that has failed to migrate properly. Goodwin said that, for now, bulk migration of customer accounts is on hold until Cubic resolves these issues.
Another key issue, Goodwin said, is malfunctioning card vending machines and terminals.
He said multiple agencies have told the MTC that some customers have been unable to register or add money to older Clipper cards and that several transit agencies are “not currently able to replace lost, stolen, or damaged Clipper cards.“
People with these issues should visit clippercard.com to order a replacement card, Goodwin said.
Finally, some people who automatically reload money onto their Clipper cards every month have found that system simply isn’t working. As this snafu impacts some of the Bay Area’s most loyal and consistent users of public transportation, they have been among the most vocal about their frustrations.
Goodwin confirmed that the pass auto-reload function was “not working consistently for migrated or new monthly passes” and that the Clipper staff is in the process of developing instructions for customers and for transit agencies.
One Reddit user, vanwyngarden of San Francisco, who gave her name as Hope, said she hasn’t been able to see her purchase history for more than a month.
“I can’t submit my reimbursement request at work… it is absolutely insane to me how this is allowed. I am so fired up,” she posted.
Hope said people like her who can’t access their passes can end up paying a full fare every two hours if they ride to multiple donations. “I just paid nearly $7 today already because I transferred a few minutes past the cutoff of having paid this morning after being late, rushing to try and figure out how I could get the pass,” she said. “I just gave up.”
She said reps answering calls at Clipper’s customer service phone line (1-877-878-8883) take a long time to pick up the phone and solve customers’ problems, if they’re able to at all. Goodwin recommended that customers continue to call that number for help.
Goodwin confirmed that some people were not seeing their cash balance on their app or website, but he said that didn’t mean the balance had gone away. The data containing people’s past payments is still in the “legacy back office” of the old system, he said.
“The rub is that the new Customer Service Center does not have direct access to the legacy system,” he said. “These issues must be investigated and fixed with assistance from Cubic,” he noted. “This bespoke process can be time-consuming, which is why bulk migration from the original system to the next-gen system has not yet begun.”
