Due to changes in climatic conditions in Poland interest in viticulture and wine production has considerably boosted. One of the worldwide trends in winemaking is use of indigenous strains of yeast and lactic acid bacteria (LAB). The aim of the study was to analyse the microbial diversity of Polish red wines and their key properties and combine them for better understanding of the processes responsible for creating the sensory attributes. Metagenetic analysis was used to characterise the bacterial and yeast diversity of wines produced by spontaneous fermentation of grapes of the Regent variety, which came from three vineyards: “Dom Bliskowice” (DB), “Małe Dobre” (MD), and “Winnica Janowiec” (WJ). Among bacteria, Tatumella ptyseos was the most abundant species in DB and WJ wines and Leuconostoc pseudomesenteroides was the most abundant in MD wine. Among yeasts, Saccharomyces cerevisiae was found in DB and WJ wines, Saccharomyces cariocanus in MD wine, and Hanseniaspora uvarum in all samples studied. Studied wines had statistically significantly different antioxidant capacities and distinct glucose, fructose, and lactic acid concentrations. The presence of acetic and lactic acid bacteria was positively related to the concentrations of acetic and lactic acid, respectively, while the lack of malic acid was indicative of malolactic fermentation. This knowledge may be useful in the development of unique local starter cultures for the production of wines with specific characteristics.