A drive unit with a cleaning module for cleaning an inventory system includes a frame, a drive module, a blower module, and at least one cleaning module mounted to the frame. The drive module includes at least two drive wheels that can move the unit, and the blower module can generate negative pressure in a debris container for applying to one or more cleaning modules. A first cleaning module includes a rotating brush and spans a cleaning path at least as wide as the drive wheels of the drive module as the drive unit with a cleaning module operates. Some cleaning-enabled drive units can include a bifurcation of the first cleaning module to avoid damaging fiducial markings in the inventory system. Such units include a second cleaning module with a stationary brush positioned in line with the bifurcation to clean the fiducial markings along the cleaning path without causing damage.