The article presents the results of thermodynamic analysis of the process of carbon dioxide absorption from flue gases with the use of the results of research carried out on an experimental pilot plant. According to the state of the art, among many process modifications, a promising solution is Heat Integrated Stripper (HIS) using built-in heat exchangers in the stripper. However, there are no experimental results available to confirm the effectiveness of this solution. The objective of the research was to compare the effectiveness of the process using a modified stripper to the standard process. Experimental research was carried out on the mobile pilot plant for amine-based CO2 capture from flue gases with a nominal flow of 200 m3/h using aqueous solutions of MEA 30% and AMP/Pz 30/10%. Due to the occurring measurement redundancy, advanced data validation and reconciliation of measurements method in the mass balancing of the carbon dioxide absorption process under the methodology included in VDI 2048 guidelines was used. Discussion of the results of the calculations obtained in different variants of the operating condition of the pilot plant was carried out. Obtained results clearly showed the necessity of using the advanced data validation and reconciliation method of measurements in the case of measurements redundancy. The research carried out showed a positive effect of the application of HIS, although the range of reduction of the energy consumption depended on the type of solution and the process configuration. The impact of heat integration was mainly seen in the favourable effect on the temperature profile of the stripper, resulting in an increase in carbon dioxide capture without additional heat consumption.