Rolled out in January UC 0078, the C-type was approved and became Zeon's mainstay mobile suit, serving for at least a full year through the early stages of the One Year War. The standard paintjob on the C-type was a combination of different greens and black, though a few ace pilots would paint their units in custom colors, such as the distinctive red of "Red Comet" Char Aznable and the black-and-purple of the Black Tri-Stars team of Gaia, Mash and Ortega, all of whom distinguished themselves during the Loum Campaign early in the One Year War. By February UC 0079, the C-type was upgraded into the new MS-06F, or "F-type," and would continue to be Zeon's standard frontline unit through the end of the war.

Following the Lourm campaign more than 700 C type Zaku II's would be stripped of their NCB armor and refashioned into F type, J type or S type models. However, a significant portion were sold on the black market to pay for this massive undertaking, the majority making it into the hands of the JDEG. As such, this mobile suit, still with its NCB armor but without its nuclear armament, has made it into the hands of many common criminals.