The extensive utilization of dyes across diverse industries has resulted in environmental pollution, leading to the degradation of water bodies. To prevent environmental contamination, the use of eco-friendly dyes and innovative processes for dye degradation is crucial. This study aimed to investigate the color removal process of cochineal dye (Dactylopius coccus Costa) using the atmospheric pressure plasma jet (APPJ: Atmospheric Pressure Plasma Jet) technique. The dye extracted from the cochineal insect was treated with APPJ and the resulting color removal process was analyzed. Optical emission spectroscopy (OES) was used to investigate the plasma emission lines, and UV-Vis spectroscopy was used to monitor the color removal process. The results revealed that the decolorization of cochineal dye was a result of an oxidative degradation process caused by the interaction of the reactive species (NO3− and NO2−) generated by the APPJ plasma discharge with the dye molecules. This color removal process occurs in an acidic medium, leading to a pH change from 5.4 to 2.7. These pH changes can be attributed to fluctuations in the concentrations of reactive species such as nitrates and nitrites in the liquid phase. UV-Vis spectroscopy measurements showed that 90% of the cochineal color was removed within the first 10 min of treatment. This study enhances our understanding of natural color removal and provides insights into its mechanism, opening up possibilities for controlled modification and applications in various fields.