Bryndza cheese is a traditional Slovakian product. In this research, we have investigated whether it would be possible to freeze bryndza, store it at a temperature of -18°C, and then thaw and place it on the market during the off-production season. The current legislation in Slovakia does not allow this procedure. The freezing process was chosen based on the request of several small food business operators who would like to replace the process of preserving the primary raw material, matured salted ewe’s lump cheese, in barrels due to acrid-sour taste. Bryndza cheese is preferred by consumers due to its unique microbial composition, which is beneficial for their health. Many microorganisms present in bryndza are probiotics. For this reason, we wanted to determine how the microflora in the bryndza cheese changes after freezing. These findings have practical implications for the food industry, particularly for small food business operators, who can potentially adopt freezing to preserve bryndza, thereby extending its shelf life and availability to consumers. Additionally, in many households, people store bryndza in their freezers after purchasing and use it to prepare dishes. Understanding the role of microorganisms in the ripening process and during storage can provide valuable data on Brynzda quality and safety. The present study aimed to analyse the representation of microorganisms in “Bryndza” samples at the beginning of storage and after 6 months of storage at a temperature of -18 °C. A total of 10 samples of “Bryndza” cheese made from pasteurised milk were analysed. Analysis of total viable counts of viable bacteria (TVC), coliform bacteria (CB), lactic acid bacteria (LAB), and microscopic filamentous fungi (MFF) was performed using the plate dilution method. Isolated strains of microorganisms were identified with mass spectrometry MALDI-TOF MS Biotyper. A total of 295 isolates from Bryndza cheese were identified at the start of storage and 220 isolates at the end of storage of samples. The dominant species of microorganisms found in Bryndza cheese were lactic acid bacteria, especially Lactococcus lactis, with 68 isolates and Lactobacillus fermentum, with 41 isolates at the start of storage. The most frequently isolated species were Lactococcus lactis, with 62 isolates, and Limosilactobacillus fermentum, with 33 isolates. Our results show that important lactic acid bacteria were present in the bryndza even after 6 months of freezing, but coliform bacteria were absent. Experimental outputs: TVC: showed no significant decrease (p-value = 0.0137); LAB: No significant decrease in lactic acid bacteria counts post-storage; MFF: Significant decrease in microscopic filamentous fungi post-storage; CB: Qualitative analysis indicates a significant reduction to undetectable levels after storage. Long-term storage of bryndza at -18°C is safe from a microbiological point of view.