The phenomenon of global warming has been demonstrated to induce the premature ripening of grapes, resulting in a concomitant increase in sugar and a decrease in acidity. This can result in the production of wines that are characterised by an imbalance in terms of alcohol content and acidity. The utilisation of lactic acid-producing Lachancea thermotolerans yeast in fermentation represents a promising strategy for reducing the pH of must without the need for chemical acidification. However, it is important to note that the fermentation rate and lactic acid production can be influenced by several factors present in the must. The present study focused on the effect of copper, used in organic vineyards to limit mildew, on biomass and lactic acid production by two L. thermotolerans oenological strains in laboratory-scale fermentations. The methodology used is based on an innovative integrative approach combining conventional microbiological, spectroscopic, cytometric and transcriptomic analyses. The results obtained demonstrated that the addition of copper increased lactic acid production in comparison with the control condition and this effect was strain-dependent, reaching up to 16.15 g/L for strain Lt1 under conditions of high copper concentration (20 mg/L). The monitoring of microbial populations demonstrated discrepancies in the fermentation kinetics in conditions exhibiting varying concentrations of copper and showed that an increased duration of cell generation is evident under conditions exhibiting elevated copper concentrations, particularly in the context of the Lt1 strain. Furthermore, the analysis of the samples using flow cytometry revealed the oxidative status of the two strains throughout the fermentation process. Transcriptomic data indicated that metabolic pathways involved in cell communication, ribosomal and cell wall activity of L. thermotolerans were modulated by the presence of copper. The findings of this study demonstrate strain-specific effects of copper on L. thermotolerans, which may be of interest to winemakers, particularly those engaged in organic viticulture who intend to use acidifying yeasts during warm vintages.