This study presents an extensive intercomparison between a benchtop X-ray fluorescence (XRF) system and near real-time XRF monitors (Xact 625 and 625i) for measuring elemental concentrations in ambient aerosols. The measurements were conducted across three locations: Athens (Greece, March 2024), Nicosia (Cyprus, March–January 2023), and Dublin (Ireland, December 2022–February 2023). The focus was on evaluating the chemical composition of particulate matter (PM) and the impact of filter substrate choice on measurement consistency. The study specifically examines the elements Si, S, Cl, K, Ca, V, Ti, Mn, Fe, Cu, Ni, Zn, Sr, and Pb. The results highlight that filter type plays a crucial role in ensuring accurate measurements when utilizing the benchtop XRF system. At the Athens site, where PTFE filters were used, the agreement between the Xact 625i and the benchtop XRF system was stronger, with slopes generally closer to unity for most elements. In contrast, quartz fiber filters at the Dublin and Nicosia sites led to systematic deviations, especially for light elements such as S, Cl, and K, even after applying correction factors. For heavier elements like Fe, Mn, and Cu, the filter effect was less pronounced, though some variation across sites remained. Zn consistently showed good agreement, while Pb exhibited weaker correlation, possibly due to differences in the calibration curves of the two systems. Overall, this study not only evaluates instrument performance across multiple environments but also provides practical guidance for mitigating filter-related artifacts to enhance consistency in elemental aerosol measurements.