Troubleshooting batch processes at a plant-wide level requires first finding the unit causing the fault, and then understanding why the fault occurs in that unit. Whereas in the literature case studies discussing the latter issue abound, little attention has been given so far to the former, which is complex for several reasons: the processing units are often operated in a non-sequential way, with unusual series-parallel arrangements; holding vessels may be required to compensate for lack of production capacity, and reacting phenomena can occur in these vessels; and the evidence of batch abnormality may be available only from the end unit and at the end of the production cycle. We propose a structured methodology to assist the troubleshooting of plant-wide batch processes in data-rich environments where multivariate statistical techniques can be exploited. Namely, we first analyze the last unit wherein the fault manifests itself, and we then step back across the units through the process flow diagram (according to the manufacturing recipe) until the fault cannot be detected by the available field sensors any more. That enables us to isolate the unit wherefrom the fault originates. Interrogation of multivariate statistical models for that unit coupled to engineering judgement allow identifying the most likely root cause of the fault. We apply the proposed methodology to troubleshoot a complex industrial batch process that manufactures a specialty chemical, where productivity was originally limited by unexplained variability of the final product quality. Correction of the fault allowed for a significant increase in productivity.