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Another headache for the holidays? Your EMV card

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With Black Friday around the corner, retailers and consumers have been forced to factor one more challenge into their holiday shopping strategy: EMV chip cards.

It is no doubt on consumers' minds: Ease of checkout is the No. 1 in-store technology shoppers want this holiday season, according to a study of 2,000-plus consumers and 230 retailers by PricewaterhouseCoopers. And 28 percent of EMV payment card users found use confusing or bothersome or avoid stores with EMV, according to a separate study by Mercator Advisory Group.

While the process to scan chips at the register is slightly longer than the traditional swipe-and-sign, the confusion around the inconsistent payment process is likely to cause more delays than the cards themselves, experts told CNBC. But it may be a small price to pay for the added security the cards provide.

"You're going to be out shopping, and sometimes it's swipe, sometimes it's chip," said Rob Cameron, chief product and marketing officer at Moneris, the fifth-largest payment processor for merchants in North America. "It's going to be hard to anticipate what they are going to do."

Indeed, consumers are still in the middle of the transition to the EMV system: In October, about 54 percent of consumers said they had at least one chip card in their wallet, Mastercard told American Banker.

Cameron, who dealt with the EMV switch that happened in Canada from 2006 to 2012, said that because the U.S. rollout has been less consistent than other countries, consumers should be prepared to watch the person in front of them in line so they can be ready to pay correctly.

Otherwise, it could feel like the equivalent of everyone in line writing a check — i.e. slow, said Eric Olafson of Demandware, which helps businesses sync their e-commerce and in-store point-of-sale systems.

"Retailers are trying to generate peak volume," Olafson said. "If you start talking about anything that slows that down, that translates into dollars."

But credit cards, of course, are not the only factor that could speed up or slow down a transaction, said J. Craig Shearman, vice president for government affairs at the National Retail Federation.

Making change, by comparison, can be a time consumer for retailers — and 39 percent of customers still use cash for holiday shopping, according to Bankrate.com study released this week. And the process of printing a receipt or signing on the line often takes longer than the card scan itself.

"It's a pretty simple process; you figure it out pretty quick," Shearman said. "It will become muscle memory. They have been used in Asia and Europe, and they don't slow down lines there."

Having a well-trained staff can help, Shearman said. Target, for example, has had its EMV systems fully rolled out since August to prepare cashiers for explaining the chip cards to first-time users, according to spokeswoman Molly Snyder.

There are also more alternatives now to standing in long lines. Though Black Friday is still the most popular shopping day, sales are now spread throughout the weekend: Black Friday sales were down 1.6 percent last year compared with those in 2013, but up 0.9 percent when looking at Thursday through Sunday of Thanksgiving weekend, Mastercard said in a survey.

Plus, online shopping and mobile payments are gaining ground among consumers, while line-busting — where a sales associate uses a mobile device like a tablet to ring you up while you wait — is also becoming more common.

But the majority of shopping still takes place in store and with traditional payment methods — meaning that for now, some deal-seekers should add "patience" to their holiday wish list. Still, for the reduced theft of identity theft, Shearman said, it's worth the wait.