In the last decade, fresh-cut plants have become a more popular flavoring additive in food. It is important to find an effective method for ensuring the safety and quality of plant materials used as food additives. Ozonated water is being considered by the EFSA for approval as a cidal agent for plant protection. The objective of this study was to evaluate the effectiveness of ozonated water in improving the microbial safety of fresh-cut parsley leaves, with a particular focus on mesophilic and psychrotrophic bacteria and fungi. The yeasts and bacteria were identified with the MALDI-TOF MS system. Color changes on the surface of the parsley samples were measured in the CIE L*a*b trichromatic color model. The chemical composition of the essential oil was evaluated via gas chromatography with mass spectrometry (GCMS). The microbial level of the fresh leaves varied and depended on the season. The highest microbial levels were found in the leaves picked in the summer and autumn, at 104 to 106 CFU/g for fungi and 106 to 108 CFU/g for bacteria. Among the isolates with the highest isolation frequency, bacteria belonging to Pseudomonas fluorescens, Staphylococcus warneri, and Bacillus megaterium dominated. The dominant yeasts and molds were Candida sp., Rhodotorula sp., Cladosporium sp., and Fusarium sp. The conditions for water ozonation (ozone dose and time) were established for both mono- and mixed cultures. Time of 3 min, ozone content of 0.5, O3 mg/L or 1 min, and 1.5 mg of O3 mg/L were sufficient for a 90% reduction in the number of living microorganisms. Yeasts and bacteria were sensitive to ozone treatment, excluding P. fluorescens rods. The tested mold strains were the most resistant. However, it was noted that organic matter might reduce the decontamination effect. The effectiveness of ozonation was negatively influenced by organic compound content above 1%. Spectrophotometric measurements of parsley leaves after ozonation, especially after 3 min treatment at 1.5 O3 mg/L, revealed morphological changes. The CIELAB color space (L*a*b*) changed in the direction of lightness and yellowness; however, ΔE showed no statistically significant differences in comparison with the untreated leaves. In preliminary studies, no differences were noted in GLC-MS chromatograms for essential oils of parsley leaves before and after ozonation. The aroma of parsley treated with ozonated water was more intensely herbal than the control sample, probably due to the higher content of α and β phellandrene. The results of this study show that decontamination of parsley leaves by ozonated water containing 1.5 O3 mg/L in a closed 5 min process can effectively ensure the microbiological quality of fresh-cut parsley leaves. It can be concluded that ozone treatments in aqueous form appear to provide promising qualitative and quantitative results for the decontamination of this fresh-cut plant material. However, more work is necessary to study chemical and volatilome changes. Especially the sensory analyses should be conducted before and after ozone treatment.