Ford Motor Co. will begin using a Linux-based operating system, called QNX, to power its Sync mobile-phone multimedia software beginning in 2016, ending its use of Microsoft Corp.'s Windows, an official with the car company said.

The move will lower Ford's costs and give them a simple system that hardware makers and other software developers are comfortable using.

Despite pioneering the move into in-car mobile technology, Ford has run into trouble with the Microsoft-based Sync in recent years as it integrated the phone-pairing system with a touch screen called MyFord Touch. Many of the bugs in the system weren't related to problems with Microsoft's platform, however.

Ford considered using a Google Inc. Android-based system, as well as Microsoft's system before settling on QNX Software Systems, which is owned by BlackBerry Ltd., according to this person.

The system is used by other auto makers to run multimedia systems that connect phones to in-car technology, allowing for voice-activated calling and radio controls, and other applications.

The decision to drop Microsoft and its Windows Embedded Automotive offering came primarily as a result of the expense of licensing the Redmond, Wash.-based company's operating system. Equipment suppliers also had a strong familiarity with the QNX system and preferred working with it, said the official, who declined to be named because the matter isn't public.

Bloomberg News earlier reported the change.

Honda Motor Co.'s Acura, General Motors Co., Hyundai Motor Co., Volkswagen AG's Audi and Porsche use QNX in their multimedia systems, according the company's website.

Ford, along with Microsoft, was a leader in pushing in-car mobile phone integration. It launched Sync in 2007 on a few models as an option and now its system is standard on most of its vehicles in many regions of the world.

Its Sync system is used on more than 7 million vehicles around the world and has become an important marketing tool for Ford.

More recently, Ford has had quality problems with its MyFord Touch system, which is a touch-screen interface and Bluetooth-activated voice control system. MyFord Touch had problems with freezing, or failing to recognize voice controls early on. Ford has been upgrading the system to work out the bugs, but most of these issues had little to do with Microsoft, the official said.

Microsoft's other major customers in the automotive industry are Fiat Chrysler Automobiles NV, Nissan Motor Co. and Kia Motors Corp, according to the company's website. A spokesman for the software company couldn't immediately be reached to comment.

A QNX spokesman declined to comment on the report, but said the company already does work with Ford.

-Shira Ovide in San Francisco contributed to this article.

Write to Mike Ramsey at michael.ramsey@wsj.com

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