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Ongoing Clipper 2.0 Issues Plague Bay Area Transit Agencies, Seniors and Low-Income Riders

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A passenger tags their Clipper card at Montgomery BART Station in San Francisco on Dec. 4, 2024. The company responsible for Clipper’s new fare payment system said that it was making progress on resolving issues, as transit agency leaders voiced their frustration with ongoing glitches.  (Juliana Yamada/KQED)

More than two months after the debut of next generation Clipper, glitches continue to plague the fare payment system, leaving transit agencies unsure of their revenue, riders guessing at how much money is on their cards and the entire project far behind schedule.

Representatives from Cubic Transportation Systems, which holds the over $400 million contract to develop and run the new payment system, also known as Clipper 2.0, appeared before the Clipper Executive Board on Monday to once again deliver a laundry list of problems with the long-awaited update, and a timeline for solutions.

“We have remaining issues that continue to affect riders, frontline staff and operators, and we take those issues seriously and continue to work to resolve specific issues with vending machines, inspection devices, and account transitions,” said Peter Montgomery-Torrellas, the president of Cubic Transportation Systems.

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Next generation Clipper promised long-awaited improvements like transfer discounts, the option to pay with a credit or debit card and the ability to apply for discounted accounts online. It’s the first major update to the Clipper system since it debuted — then known as TransLink — in 2006. But the rollout of the system has been plagued with errors that have taken months to fix, frustrating transit agencies and riders alike.

Transit riders who have been upgraded to next-generation Clipper have experienced a variety of issues, including being overcharged, the inability to access their accounts, and customer service representatives who themselves are stymied by software issues.

At Monday’s meeting, transit officials from around the region emphasized the negative effects Clipper 2.0 has had on their customers.

Mayor Daniel Lurie (left) and SFMTA Director Julie Kirschbaum (right) pose for a picture in one of the psychedelic-themed buses in the Haight Ashbury District in San Francisco on July 22, 2025. (Tâm Vũ/KQED)

“It feels to me like we have made the first next-generation Clipper users beta testers,” said Julie Kirschbaum, director of transportation at the San Francisco Municipal Transportation Agency.

The new system has also caused unreliability in the fare inspection devices used by transit agencies like Caltrain and Muni.

“If we can’t check proof of payment, that affects our ability to collect the funding that we need to run our agency,” said Jason Baker, director of government affairs for Caltrain.

Cubic acknowledged issues with fare inspection devices, including overly long transaction times, and said that it was in the process of updating the machines to fix them, with work on that front set to continue into April.

“We do fare inspections on 100-person crowded Muni buses, and that transaction time is just making fair compliance impossible,” Kirschbaum said.

Data from WSP USA Services Inc., the company contracted to staff the Clipper customer service center, indicates many customers are still experiencing issues with the system. About 2,000 Clipper customers call the customer service center each weekday, although average wait times have trended downward over the last few weeks — around 26 minutes, down from over 40.

In Clipper 2.0’s implementation, the Metropolitan Transportation Commission prioritized upgrading the accounts of users on Clipper START, a discounted fare program for low-income riders and those with discounted youth or senior accounts. People also had the opportunity to jumpstart the upgrade by calling Clipper customer service.

At Monday’s meeting, Denis Mulligan, the general manager of the Golden Gate Highway & Transportation District, lamented that those groups, in particular, have suffered the brunt of next generation Clipper’s faults.

‘For the last two and a half months, seniors trying to ride transit to see their grandkids or go to appointments have had challenges with Clipper. The same thing for poor people in our community,” Mulligan said. “They did not do anything wrong. Cubic rolled out Clipper 2.0, and they lost the ability to live their lives like they normally do.”

Passengers board a bus at the Eastmont Transit Center in Oakland on Dec. 17, 2025. (Martin do Nascimento/KQED)

The MTC originally estimated that it would take eight to 12 weeks to upgrade all Clipper users’ accounts to the new version, but as that date draws near, less than 10%of the estimated 15 million cards have been upgraded.

Initially, the MTC planned to migrate Clipper users’ accounts in large batches, but the intensity of the glitches has meant that Cubic has only been able to do the upgrades “on demand,” when customers contact customer service.

Mulligan implored Cubic to hold off on larger-batch transfers to Clipper 2.0 until all the glitches were ironed out.

“Until we address all the outstanding seniors and poor individuals who have a dysfunctioning Clipper account, we should not do bulk migration,” he said.

Christy Wegener, the executive director of the Livermore Amador Valley Transit Authority, said that at the current rate, with about seven to eight thousand accounts upgraded per day, it would take over three years to fully transition all accounts to next-generation Clipper.

Last month, BART General Manager Robert Powers said Cubic needed to make a “180-degree turn in the performance of this system and the rider experience, because if it isn’t and it’s much of the same, then it may be a bridge too far to recover from.”

At Monday’s meeting, it appeared that threshold had not been reached, although some board members suggested that after the dust settles, the MTC should review what went wrong with Clipper 2.0.

“What went wrong from when Clipper 2.0 was tested to whoever made the decision and said ‘Yes, let’s go live?’” said Danielle Schmitz, executive director of Napa Valley Transportation Authority, who indicated support for an “after-action review.”

Cubic has laid out a timeline for resolution of existing problems, with most expected to be solved by mid-March. The company said that less than 1% of the 920,000 cards that have been upgraded to next generation Clipper still have issues.

In the meantime, some transit agencies reported being skittish about recommending Clipper to riders during high-profile events, a choice made all the more consequential by the looming budget crisis for many of them.

“During the Super Bowl or anything that whole week, we really just sort of focused on [tap to pay debit and credit cards,]” said Carolyn Gonot, the general manager of the Santa Clara Valley Transportation Authority. “Buying Clipper cards was a little nerve-racking because we didn’t know if they would work.”

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