A container transferring system autonomously transfers a container between a product processing machine and a container storage position. The system includes an automated guided vehicle (AGV) container transferring subsystem, and a machine side container conveying subsystem. The machine side conveying subsystem is arranged adjacent the product processing machine and receives empty containers from the AGV container transferring subsystem and transmits a full container to the AGV container transferring subsystem. The AGV container transferring subsystem docks with the machine side container conveying subsystem at a first docking position and moves autonomously between the first docking position and the container storage position to transport the empty container from the container storage position to the machine side container conveying subsystem, and transport the full container from the machine side container conveying subsystem to the container storage position.