An integrated data reader and electronic article surveillance (EAS) system, and methods of operation. In one configuration, a data reader such as a bar code scanner is equipped with an EAS deactivation module disposed behind the scanner surface preferably downstream and/or upstream of the scanner window. The system may be configured such that the EAS deactivation module is interchangeable from the right side of the scanner housing (which is preferred for left-to-right scanning motion) to the left side of the scanner housing (which is preferred for right-to-left scanning motion). In other configurations, the deactivation module may be disposed in the housing adjacent to the window and oriented longitudinally and parallel to the sweep direction of the item. The EAS deactivation modules have various configurations such as simple planar coils, a magnetically active core with coil windings, or two part L-shape construction.