Bioaerosols can be effectively entrapped within the porous structure of HVAC filters. Nonetheless, conventional filters do not inactivate accumulated/multiplied microorganisms on the filter media, increasing the risk of pathogen release downstream. To address this challenge, this study presents a fanless, energy-efficient technology for the thermal disinfection of filters. During disinfection, buoyancy-driven flow transfers heat to the filter, eliminating the need for recirculating fans and the reliability and maintenance concerns associated with elevated-temperature operation. The system consists of two identical parallel units, each containing a MERV 11 filter and tubular heating elements. To reduce the temperature non-uniformity inherent to natural convection, three system configurations were experimentally investigated over a range of heater set-point temperatures. The configurations differed in filter housing design and the arrangement of heating elements. A literature-based thermal criterion of 65 °C for 10 min was used to determine the required disinfection time and energy. Moreover, the filtration performance and flow resistance of the system were evaluated using an ASHRAE 52.2-compliant wind tunnel at three air velocities (0.5, 0.75, and 1 m/s). The results revealed that the optimal configuration substantially reduces thermal non-uniformity across the filter, enabling the entire filter to reach the disinfection condition within approximately 35 min, with an energy demand of 0.10 kWh. Furthermore, flow characterization tests indicated that the presence of heating elements and duct modifications does not significantly affect filtration efficiency and results in a minor increase in pressure drop during normal filtration operation.