This article constitutes a continuation of "Exergy analysis for a power plant alternative designs, Part I." In this article the analysis of the 95 MW cogeneration unit is performed and a comparison between the existing unit and the proposed cogeneration unit is made. The analysis and the comparison will be based on fuel cost, operation and maintenance costs, reliability, and air emissions of each case. All necessary data are obtained from the existing power plants (steam, gas turbine and diesel fuel) located at Linoperamata, Crete. Data for the cogeneration unit are obtained from the similar unit located at the town of Chania, Crete. Exergy analysis is used for the evaluation of the proposed solutions.