Spore-forming bacteria in food are a major cause of food spoilage or food poisoning, leading to economic burden. Even after a heat treatment, surviving spores could be able to recover. The recovery consists of different physiological stages: germination, outgrowth and the first cell multiplication. The sporulation conditions, heat treatment intensity and recovery conditions have an effect on spore recovery ability and recovery kinetics. Nevertheless, the physiological stage which is the most impacted by the recovery conditions and the heat treatment intensity remains unclear. To quantify the impact of sporulation condition, heat treatment intensity and recovery conditions on the different recovery stages, recovery kinetics were performed using flow cytometry. The transfer from a physiological stage to the next one was monitored thanks to size and fluorescence intensity of cells which are labeled with Syto9 (permeability of spores) or 5-Cyano-2,3-ditolyl tetrazolium chloride (CTC, respiratory activity). Sporulation and recovery conditions could highly impact the yield and time of germination. The heat treatment impact is more complex as spores can be altered by various ways. It could be put in evidence by using cell criteria as size, Syto9 and CTC fluorescence intensity. Flow cytometry enables the quantification of the impact of sporulation, heat treatment and recovery conditions on the different stages during spore recovery. It allows the analysis of a large number of events over time and to discriminate what stage(s) is (are) the most impacted by each condition.