Systems and methods are provided for an integrated air filter assembly for a multiple fuel cell powertrain. The integrated air filter assembly can include a common inlet to pull air from a single plenum of the hood, where the intake path can be split into multiple ducts providing air flow into each respective fuel cell. Each duct can include a dedicated air filter to filter the incoming air. The assembly can also include flexible seal to adapt to the unique hood/plenum shape of different OEM plenums/intakes.