This paper describes a methodology to establish an optimal process design for prickly pear wine production that preserves the peculiar and unique traits of traditional products, generating at the same time, technical information for appropriate design of both bioreactor and overall process. The strategy includes alcoholic fermentation optimization by the mixed native culture composed by Pichia fermentans and Saccharomyces cerevisiae, followed by malolactic fermentation optimization by Oenococcus oeni. The optimization criteria were based on multiple output functions: alcohol content, volatile compounds profile, organic acids profile, and compound contents related to color, which were analyzed by spectroscopy–chromatography methods and sensory analysis. The results showed that the mixed culture inoculated into a bioreactor containing prickly pear juice with 20 °Bx of fermentable sugars concentration, processed at a constant temperature of 20 °C for 240 h, leads to a fermented product with 9.93% (v/v) total alcohol content, and significant abundance of volatile compounds, which provide fruity and ethereal aromatic notes, complemented by a lively but not unpleasant acidity. This young wine was further subjected to malolactic fermentation at constant temperature (16 °C) for 192 h, decreasing malic acid, and balancing volatile compounds contents, thus resulting in a product with better aroma and flavor perception, and a velvety feeling of long aftertaste. Repeated assays showed that the process is stable, predictable, controllable, and reproducible. These results were used for process design and spreadsheet construction in order to simulate the process, and properly select and size the equipment required for such process.