Best Buy Co. said it would join the growing list of retailers accepting Apple Pay this year, undercutting a merchant-led group that had hoped to beat Apple with its own mobile-payment system.

Best Buy's mobile app now accepts Apple Pay online, though physical stores won't get the service until later this year. A Best Buy spokesman said the chain needs time to update its own checkout systems. Apple Inc. mentioned the electronics retailer's participation during its quarterly earnings call Monday.

The deal complicates the future for Merchant Customer Exchange, a consortium of retail chains that plans to roll out its own payment system called CurrentC sometime this summer. Best Buy was a founding member of the group, also called MCX.

MCX members have pledged in the past not to accept mobile payments from other sources. But Best Buy on Monday said it would remain a member of the group even as the chain opens up its cash registers to Apple.

MCX Chief Operating Officer Scott Rankin said the exclusivity agreements that tied members to CurrentC will lapse in the second half of this year, an acknowledgment that the service will have to compete with one or two other payment systems in the future.

"At some point later this year our exclusivity period ends so there would obviously be no issues there," Mr. Rankin said in an interview. "We would obviously love to go faster, but we want to make sure when we build this thing, we build it right."

Wal-Mart Stores Inc., also a member of MCX, said earlier this year that it was open in theory to different payment options including Apple Pay.

Apple launched its payment system on its newest iPhones last year. The system stores users" credit card information on the iPhone and verifies the purchaser using a fingerprint scanner.

Write to Drew FitzGerald at andrew.fitzgerald@wsj.com

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