This study aimed to assess the safety characteristics of organic high-protein bars (HPB) during storage at ambient and refrigerated temperatures based on selected microbiological and chemical indicators. After production, the total number of microorganisms ranged from 3.90–4.26 log CFU/g;. The Enterobacteriaceae family was present at 2.81–3.32 log CFU/g, and the count of yeasts and moulds was 2.61–3.99 log CFU/g. No Salmonella sp. was found in 25 g of the product. Bacillus cereus was present in samples B1 and B2. Staphylococcus aureus was presented in samples below the detection limit (<2 log CFU/g). During the storage of products, the number of microorganisms varied. After production and storage, in all samples of HPB, the amount of mycotoxins was below the detection limit. The presence of histamine and tryptamine was not found in the HPB throughout the study period. Regarding TBARS, it can be concluded that the use of prunes and oat flakes (B2 bar composition) in the production of organic bars, and refrigerated storage, reduces the degree of fat oxidation. Among the tested variants, the composition of the B3 bar seemed to be the safest and worth further research, mainly due to the lower frequency of undesirable microorganisms. The protective antioxidative effect of prunes and oat flakes in bars stored at 22 °C indicates the value of the composition of bar B2. The appropriate composition modifications and the use of heat treatment proved to be effective in improving the safety characteristics of HPB. Relying on the results it is possible to store HPB for at least 3 months. Next to standard safety parameters, the unique and effective to increase the safety of HPB is controlling the presence of B. cereus and other low water activity (aw) resistant microorganisms.