Sanitation Standard Operating Procedures (SSOP) are critical in key stages of food production and processing. After manufacturing, slicing process can serve as a point of contamination, potentially compromising the quality and shelf life of mozzarella. The objective of this study was to determine the effect of SSOP on the quantification and diversity of psychrotrophic bacteria with proteolytic and lipolytic potential in mozzarella before and after industrial slicing. Psychrotrophic bacteria were isolated, phenotypically assessed for spoilage potential under mesophilic and psychrotrophic conditions, analysed for diversity using dendrograms of genetic similarity and identified by partial sequencing of the 16S rRNA gene. The mean psychrotrophic counts were 3.77 (±0.83) log CFU/mL before slicing and 3.58 (±0.51) log CFU/mL in the sliced product, indicating a non-significant reduction (p < 0.05). Regarding spoilage potential, none of the 233 isolates evaluated exhibited proteolytic activity under psychrotrophic conditions. However, psychrotrophic lipolytic activity was predominant both before and after slicing. The species Lactobacillus delbrueckii, which is part of the saccharolytic inoculum used to reduce the pH of the curd during cheese production, was the main proteolytic bacteria under mesophilic conditions (35°C) in both before and after sliced samples. Although the bacterial counts indicated the full efficiency of the slicer’s SSOP, the microbial diversity analysis revealed the inclusion of Staphylococcus succinus, Staphylococcus hominis, Enterococcus faecalis and Klebsiella pneumoniae during the slicing process, albeit at low levels. Therefore, relying solely on psychrotrophic quantification may not be sufficient to attest the efficiency of the slicer’s SSOP. Even under controlled industrial conditions, spoilage bacteria from handling and environmental sources may be introduced into sliced mozzarella. Methods for improving the microbiological quality of the mozzarella pieces prior to slicing, as well as the intensification of sanitary procedures, must be reviewed and implemented to improve the shelf life and commercial potential of sliced mozzarella.