The climate changes currently manifesting pose a significant challenge for the international research community. The global environment and public health have been impacted on a global scale by the emission of greenhouse gases resulting from the combustion of fossil fuels. The increasing utilization of alternative clean resources for electricity generation is widely regarded as a promising approach to mitigate greenhouse gas emissions. Renewable energy resources are dedicated to achieving a state of zero emissions. The utilization of Proton Exchange Membrane Fuel Cell (PEMFC) technology presents itself as a viable alternative for the development of environmentally sustainable energy systems. Methanol exhibits considerable potential as an environmentally friendly fuel alternative in the realm of power generation. Methanol can be derived from both renewable and non-renewable sources, such as biomass, electrolysis, CO2 capture technology, and natural gas. The objective of this study was to reduce dependence on conventional diesel and using methanol as a fuel source through practical experiments on emissions and efficiency. The comparison was made between a Fuel Cell system using methanol as its primary fuel source and a diesel generator operating on conventional diesel fuel. The study was conducted experimentally based on the experimental setup installed in the Renewable Energy Hybrid Station at SQU. The study found that the diesel generator produced significantly higher emissions compared to the fuel cell. Specifically, the carbon dioxide emissions from the diesel generator nearly doubled, increasing from 208.18 g/kWh to 490.62 g/kWh, while carbon monoxide emissions ranged between 1.494 kWh and 0.892 kWh. Also, the nitrogen monoxide emissions increased gradually from 0.577 g/kWh to 2.043 g/kWh, and nitrogen dioxide emissions varied between 0.1923 g/kWh and 0.0065 g/kWh. In addition, the nitrogen oxides emissions were raised from 1.212 g/kWh to 3.531 g/kWh and the sulfur dioxide emissions were differed between 0.098 g/kWh and 0.016 g/kWh. The carbon dioxide emissions of the fuel cell ranged between 3.31 g/kWh & 5.09 g/kWh and the carbon monoxide emissions were varied between 0.00317 g/kWh and 0.0164 g/kWh. Furthermore, the nitrogen monoxide emissions ranged between 0.0000775 g/kWh & 0.0000755 g/kWh and nitrogen dioxide emissions differed between 0.0000236 g/kWh and 0.0000480 g/kWh. Besides, the nitrogen oxides emissions were increased from 0.0001011 g/kWh to 0.0001235 g/kWh and the sulfur dioxide emissions were not available in the chemical reactions. Moreover, the efficiency of the diesel generator ranged between 10.74% & 22.95%, and the efficiency of the fuel cell ranged between 28.33% & 27.06%. In addition, the fuel consumption of the diesel generator ranged from 0.95L & 2L and the fuel consumption of the fuel cell was ranged from 1.9L & 6.12L. The findings indicated that the methanol-based power generation system exhibits promise as a fuel source, thereby reducing dependence on diesel fuel. The fuel cell system demonstrates lower emissions in comparison to the diesel-based power generation system, while also exhibiting superior efficiency.