The packaging industry is one of the most important parts of agricultural products processing. A popular method of increasing the shelf life of agricultural products is modified atmosphere packaging (MAP). The main objective of this paper was to increase the adaptability and flexibility of the machines for packaging of different vegetables including lettuces, broccolis, cabbages, cauliflowers, etc. To achieve this goal, a supervisory control and data acquisition (SCADA)-based system was designed and developed for controlling and monitoring of MAP process of fresh vegetables. The system was divided into three physical layers: field devices, remote terminal unit (RTU) and master terminal unit (MTU). For packaging width adjuster system, the R2, maximum error (ME), mean absolute error (MAE) and root mean square error (RMSE) were obtained as 0.999, 8 mm, 2.96 mm and 3.44 mm, respectively. For packaging height adjuster system, the R2, ME, MAE and RMSE were obtained as 0.994, 10 mm, 3.53 mm and 4.57 mm, respectively. The SCADA system can be able to accurately adjust the speed of the conveyor and the temperature of the sealing jaws, based on the desired values. For gas injection unit, the value of 1.66 L/min, 0.557 L/min and 0.667 L/min were recorded for ME, MAE and RMSE, respectively. Four types of trends including temperature, speed, flow and digital parameter trends were designed. In addition to displaying screen alarms, the occurred alarms are stored, automatically as a text file for troubleshooting. Finally, the results showed that the designed system can be reliably used for MAP of various varieties of fresh vegetables.