Modifying system configuration data. At least some of the illustrative embodiments are methods including changing operation of a program on a computer system that comprises a native operating system stored on a long term storage device. In some cases, the changing by: reading system configuration data of the native operating system, the reading by a scan program executed under a non-native operating system booted on the computer system; identifying, by the scan program, the program on the long term storage device; and modifying, by the scan program, the system configuration data of the native operating system such that the change in operating of the program is implemented on a subsequent boot of the computer system under the native operating system.