This article addresses an integrated lot-sizing and scheduling problem that arises in the primary manufacturing phase of a pharmaceutical supply chain. Multiple pharmaceutical ingredients and their intermediate products are to be scheduled on parallel and capacitated bays for production in batches. Sequence-dependent setup times and costs are incurred when cleaning a bay during changeovers between different product families. The problem also contains a high multiplicity asymmetric traveling salesman-type of substructure because of sequence-dependent setups and special restrictions. Mixed-integer programming formulations are proposed for this problem and several valid inequalities are developed to tighten the model. A column generation method along with a decomposition scheme and an advanced-start solution are designed to efficiently derive good solutions to this highly complex problem. A computational investigation is performed, based on instances that closely follow a real-life application, and it demonstrates the efficacy of the proposed solution approach.