Plasma as a promising technology has recently drawn considerable interest for decontamination of food and food processing at low temperature. Also, some conventional methods are used to prevent the changes in product quality with stopping their enzymatic activity. In this paper, two plasma systems were used to study a novel method in enzyme deactivation. First a DBD system was used to process the tomato extract and determine the processing time and gas type (air and helium). Later, a gliding plasma system was used, first time, for direct processing of both sides of tomatoes due to the low penetration of DBD plasma into the product and restrictions on its formation. In the optimum case, processing time was investigated as the most important parameter and, within 7 min, the enzyme residue percentage reached 4.84%. Comparison of plasma technology with other blanching methods indicated higher plasma efficiency during the processing time. The product temperature reached the maximum 40 °C during the plasma processing, which prevented the destruction of product’s nutrient content. This study proves the capability of cold plasma technology for inactivating of enzymes.