Systems, methods, and non-transitory computer-readable storage media which have instructions stored for execution on a processor, for automating the commissioning of a transport network element within a network. A system configured according to this disclosure can be an Automated Commissioning Tool which can initiate communications with a network element on the network. The Automated Commissioning Tool can then retrieve updated firmware corresponding to the network element and configure the network element to have the updated firmware. Finally, the Automated Commissioning Tool can determine, from a network plan, a first port on the network element which is to be connected via a cross-connect to a second port on the network element and establish the cross-connect on the network element. At this point the network element may be commissioned to operate as a transport network element within the network.