The non-thermal plasma (NTP) technique is an advanced oxidation technology (AOT) applied to the degradation of organic compounds in water. In this study, the degradation kinetics of indigo carmine was investigated systematically, applying N2-NTP, O2-NTP, ozonolysis and hydrogen peroxide and the results were compared. The transient species (OH, O and NO radicals) formed with the NTP discharge at the gas-liquid interface and their products (NO3−, NO2−, H2O2) stabilized by the water, were identified and quantified. These species contribute to the effects on the chemical characteristics of the water, such as a decrease in the pH and increase in the conductivity and redox potential. Additionally, the stabilization of the oxidative species was estimated from the degradation reactions induced by the post-discharge effect, which was significant in the case of N2-NTP, due to the presence of long-lived species, such as nitrite and nitrate. The kinetics study revealed first-order kinetics for IC color removal and the rate constant values followed the order: O2-NTP (3.0 × 10−1 min−1) > O3 (1.4 × 10−1 min−1) > N2-NTP (2.2 × 10−2 min−1) > H2O2 (negligible). Also the main by-products of N2-NTP, O2-NTP and ozonolysis degradation reaction were identified by ultra-fast liquid chromatography coupled with mass spectrometry. The route fragmentation showed the formation of indole intermediates, such as isatin, which is an important precursor in organic synthesis. Display omitted •The species OH.• and NO• formed with the NTP discharge were identified•Degradation rate as follows: O2-NTP > O3 >, N2-NTP > H2O2.•Post-discharge effect was significant for N2-NTP.•IC degradation by-products identified were similar for O2-NTP, O3 and N2-NTP.