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Marin Transit has discontinued free transfers for cash-paying riders and its paid youth pass to encourage travelers to use Clipper cards.

Free transfers on Marin Transit buses will still be offered, but only for Clipper card users or those who pay with bank cards. Those riders also get free or discounted transfers of up to $2.85 on rides from any other Bay Area transit operator.

The agency will still offer its free youth passes for income-qualified riders. The paid youth passes are being transferred to the Clipper card, but with some changes.

The board voted unanimously at its meeting on Oct. 5 to approve the fare changes.

“The fare policy changes support the transition to the next-generation Clipper system and benefit our riders by offering lower fares, integrated transfers and faster, more seamless payments that reduce boarding and overall travel times,” said Marin County Supervisor Mary Sackett, president of the Marin Transit board.

The long-planned fare overhaul was bogged down by delays and glitches in the “next generation” Clipper system rollout. Clipper is a digital payment program run by the Metropolitan Transportation Commission for transit providers in the nine-county Bay Area.

Youth riders have been unable to purchase the former youth pass since Oct. 6. The free transfers for cash-paying riders end on Jan. 1.

Robert Betts, general manager of Marin Transit, said staff have been engaging riders at popular stops and transfer locations to encourage the switch.

Starting in January, staff will begin handing out free cards loaded with $5 along with materials about Clipper programs and benefits.

“I think it’s important for us to not only give away that Clipper card and allow that rider to start to use Clipper, but to also understand how to register that card, how to add value to that card and also how to take advantage of some of the fare subsidy programs,” Betts said.

Using Clipper gives adult riders an automatic 10% discount on Marin Transit, so the standard $2 fare costs Clipper users $1.80.

The upgraded Clipper system also includes a tap-and-ride feature that enables Clipper account holders to pay for the fare with credit cards, debit cards and mobile wallets.

It also includes discounted interagency transfers; the ability to instantly add and use value on a Clipper card; and the ability for families to manage multiple accounts through an app.

Marin Transit fare assistance riders who receive free bus passes have been upgraded to the new Clipper card. Marin Transit’s 31-day bus pass is now available on the Clipper system.

The frequent-rider maximum program is also available on Clipper. Those enrolled will never pay more than $5 per day or $40 per month, no matter how many times they ride Marin Transit buses.

Several other Clipper card discount programs are available.

Clipper youth cards offer a 50% fare discount for riders ages 5 to 18. The Clipper senior card offers 50% discount off adult fares and off the 31-day pass for riders 65 and older. The Clipper access card for people with disabilities offers 50% of fares. The “Clipper START Card” is an income-based program that provides 50% off single-rides for eligible riders.

If riders are using cash to pay because they don’t have bank cards, they can still load Clipper cards with cash at kiosks at the San Rafael Transit Center and at Walgreens and Whole Foods stores.

Marin Transit is planning an online informational session at 2 p.m. Thursday so riders can learn about Clipper. Meeting information is at MarinTransit.gov.