Abstract Contract Development and Manufacturing Organisations (CDMOs) are becoming a key element in the pharma and fine chemical industries during the development and production of precursor components. Most CDMOs provide their services to several companies, having to operate and organise several production lines simultaneously, complying with specific production and product requirements for each customer. Under this scenario, the operation of CDMOs depends on market changes as well as customer and product regulations, these conditioning the definition and optimization of operational plans, and in turn, hindering the definition clear routines for workers. Ultimately, the difficulties may cause planning inconsistencies, generating production delays or disruptions. For that purpose, here we present a novel methodology able to automate the scheduling and worker-task allocation for several simultaneous production lines. This is done through the sequential application of specifically designed scheduling and allocation optimization models, first identifying the optimal periodic production plan and then finding the optimal transition from current to optimal operation conditions. This approach has been applied to a real industrial process with several simultaneous production lines, successfully identifying periodic production strategies and optimal transition and worker-task allocation plans for the different lines. Overall, the proposed tool presents a first step towards the automatic integrated optimisation of production planning in fine chemical and pharmaceutical multi-purpose production plants.