The new system is like other mobile payments systems; it features a Groupon-branded credit card reader, which attaches to an iPhone or an iPod Touch via the audio jack. Merchants can accept credit and debit cards by swiping them through the card reader, or they can key in the transactions on the device's touchscreen, though charged at a higher rate.

also offers a card-reading phone case, similar to what Apple uses in its retail stores. The audio jack card reader is free, but the phone case costs $100.

What makes Groupon's new service stand out are the rates, the lowest of any payments processor on the market, with a "lowest rate guarantee" available to U.S. merchants. If merchants can provide proof of lower third-party rates for identical services, Groupon says it will lower its rates.

Groupon's rates are as follows:

Swiped transactions for MasterCard, Visa, and Discover will be charged 1.8 percent plus $0.15 per transactions.