This study addresses the optimization of the bottling process in the wine industry, focusing particularly on the filtration stage, which accounts for approximately 30% of the total costs in the value chain. In the context of significant global production, but with challenges arising from declining demand and increasing costs, precise planning becomes necessary to ensure product quality and operational efficiency in order to control and minimize the costs associated with resource usage. The work proposes an operational approach based on a mixed-integer programming model that optimizes the sequencing of batches on the filtration and bottling lines, integrating setup times that depend on the processing order. An analysis of prevailing practices in the Chilean wine industry is conducted, complemented by a literature review that identifies knowledge gaps, particularly regarding the influence of the wine’s physicochemical properties and the potential for filter blockage. The results of the model allow for reduced processing times and improved batch allocation, highlighting the importance of considering hydraulic and operational variables for more precise planning. Furthermore, the study discusses the limitations of the current approach and suggests future directions to continue optimizing production processes in the wine industry.