Quartz Crystal Microbalances (QCMs) are versatile sensors employed in various fields, from environmental monitoring to biomedical applications, owing mainly to their very high sensitivity. However, the assessment of their metrological performance, including the impact of conditioning circuits, digital processing algorithms, and working conditions, is a complex and novel area of study. The purpose of this work is to investigate and understand the measurement errors associated with different QCM measurement techniques, specifically focusing on the influence of conditioning electronic circuits. Through a tailored and novel experimental setup, two measurement architectures—a Quartz Crystal Microbalance with dissipation monitoring (QCM-D) system and an oscillator-based QCM-R system—were compared under the same mechanical load conditions. Through rigorous experimentation and signal processing techniques, the study elucidated the complexities of accurately assessing QCM parameters, especially in liquid environments and under large mechanical loads. The comparison between the two different techniques allows for highlighting the critical aspects of the measurement techniques. The experimental results were discussed and interpreted based on models allowing for a deep understanding of the measurement problems encountered with QCM-based measurement systems. The performance of the different techniques was derived, showing that while the QCM-D technique exhibited higher accuracy, the QCM-R technique offered greater precision with a simpler design. This research advances our understanding of QCM-based measurements, providing insights for designing robust measurement systems adaptable to diverse conditions, thus enhancing their effectiveness in various applications.