Among food ingredients, concentrates of lactic acid bacteria are widely used as starters for producing cheeses, fermented milks, meats, vegetables and health benefit products (probiotics). This requires the stabilization of microorganisms allowing long term conservation and the best recovery of functional properties at the moment of product’s use. Lactic acid bacteria production involves many unit operations: fermentation, cooling, concentration, formulation, freezing or freeze-drying, storage, transport between producers and users and reactivation of the stabilized micro-organisms for end-using (thawing, rehydration). Freeze-drying is known to be an energy-intensive process whereas freezing appears as a more eco-friendly alternative. However, environmental impact of storage and transport at very low temperatures (-40°C and below) may counterbalance such hypothesis. This work aims at analyzing such production system by using environmental Life Cycle Assessment (LCA) to identify hotspots and compare different existing scenarios. LCA has been performed on the basis of collected data at laboratory scale, completed by databases. SimaPro (V8.0.5 PRé consultant) has been used for the LCA modeling with ILCD 2011 method. Since freezing, freeze-drying and storage damage the lactic acid bacteria, the impact scores have been weighted by the final bacteria quality, i.e. their physiological state, to obtain meaningful comparisons. This work revealed that freeze-drying, frozen storage and fermentation were the hotspots to master the environmental impact of the system. Since freeze-dried bacteria can theoretically be stored at ambient temperature, the relevance of such a scenario was also evaluated as an option to decrease the environmental impact. However, due to bacteria quality losses, it was not found to be relevant. Finally, by comparing scenarios, it was found that the choice of the stabilization process to be used (freezing or freeze-drying) was depending on the storage duration that would be required for the product. Such a study highlighted the relevance of a Life Cycle Assessment approach to provide valuable improvements in the management of the system.