The production of wines with low biogenic amine (BA) concentrations is a current concern in the wine sector, and strategies to avoid the formation of BAs during winemaking are of particular interest. The aim of this work was to determine the influence of selected autochthonous Oenococcus oeni lactic acid bacteria (LAB) on the BA content in red wines and their prevalence against the indigenous microbiota to avoid BA formation. Sixty-seven red wines were produced at industrial scale under real winemaking conditions for three consecutive vintages. For each wine, we determined LAB implantation and the BA concentrations at various stages of the winemaking process. The results clearly indicated that the use of selected O. oeni strains that are unable to produce BA, in combination with adapted biomass production, is a good strategy to control histamine production in wines. These practices, carried out over three consecutive years, were also observed to ensure the persistence of the selected autochthonous O. oeni strain (CECT 9749) against other indigenous microbiota in the entire winery. Furthermore, analysis of BA content during wine aging in barrels indicated that low BA content was maintained, resulting in healthier wines for the consumer.