In the present study, long term performance of an HT-PEM fuel cell based micro CHP system, considering the degradation within the HT-PEM fuel cell stack and the steam methane reformer has been investigated. The variations in the generated electrical and thermal power and the corresponding efficiencies, in the first 15,000 h of operation of the plant, have been studied. Two strategies have been proposed and applied in order to remedy the excursion of thermal and electrical generation of the plant from the steady state production. In the partialization strategy, by means of reducing the fuel fed to the system, the thermal generation of the plant is kept in a specified range. On the other hand, in the recovery strategy, the supplied fuel is gradually increased to suppress the progressive reduction in the power production. The long term performance analysis of the system in normal condition reveals that, due to the degradation within the system, the power production diminishes from 28.2 kW to 23.4 kW while the thermal generation increases from 52.4 kW to 57.5 kW. The results of partialization strategy show that, in order to confine the thermal generation amplification, the partialization factor should be increased up to 7.2%. On the other hand, in the recovery strategy, the supplied fuel should be progressively increased up to 34.2% in order to preserve the electrical output at the initial level. Nevertheless, the recovery strategy has an adverse effect on the electrical efficiency as it diminishes the obtained efficiency to 21.6% compared to 24% obtained for the normal operation. In the last part of the study, the overall performance indexes of the plant, while operating in normal condition and under operational strategies, are compared. It is shown that operating under recovery strategy results in overall electrical efficiency of 24.7% which is notably lower than efficiencies of 26.1% and 26.4% obtained by operating in normal condition and under partialization strategy respectively. However, it was also demonstrated that applying this strategy results in generation of 422.6 MW h of electrical energy which is higher than the values obtained by normal operation (381.3 MW h) and partialization strategy (369.8 MW h).