At the core of Power-to-X (PtX)systems Power-to-Hydrogen (PtH) technology which produces hydrogen through electrochemical electrolysis plays a crucial role. Due to the rising global demand for hydrogen and the growing need to store variable renewable energy sources, the development of technologies to convert renewable energy into hydrogen is increasingly essential. Electrolysis as a clean and efficient process that uses DC current which is converted from the AC output of renewable energy resources to split water into hydrogen and oxygen is vital for producing green hydrogen and enabling long-term energy storage. However, integrating large-scale PtX systems into existing energy grids introduces significant power quality challenges that must be addressed to ensure reliable and stable grid operations. These challenges will become more critical as investigations show that PtX will account for 50% of future electrical consumption. Therefore, harmonic analysis will need to be strengthened in relation to summation rules, harmonic modeling and future power system design. This study proposes a comparative analysis of control frameworks for harmonic filtering in a PtH energy conversion system using the AC/DC universal diode bridge-based topology. This topology is widely used in industrial applications due to its low cost, simplicity and robustness. In order to enhance the power quality of the simulated PtH energy conversion system, two different types of control frameworks for harmonic filtering are designed in this paper. Simulation results demonstrate the effectiveness of the proposed harmonic filtering schemes, utilizing the presented control frameworks to improve the power quality of the power conversion system. Furthermore, a comparative investigation and discussion of the designed harmonic filtering schemes shows the impact of the control frameworks on power quality improvement and the resulting AC side signal after modifications. Based on the results of this paper, the most efficient control framework is selected and an extended version of the active filter equipped with this control scheme will be utilized in the full-scale experimental setup at Aarhus University's research laboratory in Foulum. These findings demonstrate the importance of the power conversion system in PtH plants and the potential for enhancing power quality through the implementation of advanced power compensation devices.