Petri nets are robust mathematical tools for the modelling, handling, and control of deadlock problems in automated manufacturing systems (AMSs). Several methods have been proposed to prevent deadlocks in AMSs. However, it is important to convert the controlled system represented by Petri nets into the program of a programmable logic controller (PLC) for the implementation of automation tasks. This study proposes a methodology based on Petri nets for deadlock prevention, and generates PLC codes for an AMS. In the suggested methodology, a Petri net model of an uncontrolled system is built, and the controlled Petri net model is developed using a deadlock-prevention method. The controlled Petri net model is then transformed into an automation-controlled Petri net model, which is further converted into a controlled token-passing logic model. The controlled token-passing logic model is utilised to generate the ladder diagrams for the AMS under consideration. The proposed methodology was tested using a real-world AMS at King Saud University labs. It provides an effective method for PLC implementation from a controlled system model represented by Petri nets.