A flexible inspection system includes a robot with a plurality of scanners and a robot controller. The robot controller is configured to receive a vehicle inspection protocol (VIP) for a vehicle being assembled on an assembly line. The VIP includes checkpoints to be scanned on the vehicle and the checkpoints correspond to components installed on the vehicle and connections between components installed on the vehicle. The robot controller commands the robot to move the plurality of scanners per the VIP such that the checkpoints are scanned. A characteristic of each checkpoint is recorded and compared to a reference characteristic such that a pass or no-pass determination of each checkpoint is provided. A vehicle inspection report with the pass/no-pass determinations is provided to an operator such that operator inspections and/or repairs of the checkpoints are made.