Air filtration systems and methods for HVAC units in transport compartments are provided. The air filtration systems and methods described herein use electrostatic forces to capture airborne particles and include a modular design so as to be configured to the space requirements of the transport compartment and reduce air flow resistance. The air filtration system includes one or more modular filtration units. Each of the modular filtration units includes a pre-filter section, an ionizing section and a collecting section.