The successful use of indigenous strains as starter cultures is dependent not only upon their capacity to complete a fermentation but also on their ability to dominate the fermentation. Chinese strain NX11424 was identified as an indigenous Chinese wine strain with commercial potential. Fermentations to assess the ability of NX11424 to compete with a commercial strain, Montrachet (UCDVEN 522), in pure and co-inoculations were performed with exo- and endo-metabolomic analyses. Metabolome analysis was run at three time points (days 2, 4 and 6). The metabolic profiles of all three treatment were similar at day 2. The endo-metabolome of the co-culture most closely resembles that of Montrachet strain at days 4 and 6, while exo-metabolomic data most closely resembles the NX11424 strain at day 6. The levels of key biomarkers among different fermentations varied at different time points, especially in amino acid metabolism; however glycerolipid, sucrose and starch metabolism were consistently most impactful in driving differences across treatment. Sulfur metabolism was also differential among treatments, with higher levels of associated metabolites in Montrachet strain. This study demonstrated the effects of pure and co-starter fermentations on cellular and wine metabolites, which can be helpful for control of wine fermentation and management of desirable wine flavor.