Infectious skin diseases are quite common in veterinary medicine. These diseases can be caused by both bacteria and pathogenic fungi. Antimicrobial drugs are usually used for treatment. An alternative to these drugs could be ozonated oils with antibacterial and antifungal properties. Four different ozonated oils (linseed, hemp seed, sunflower, and olive) were tested in order to develop an optimal pharmaceutical form for the treatment of skin infections in animals. Chemical parameters such as acid and acidity value, iodine and peroxide value, viscosity, and infrared spectres were analysed. The ozonation of oils resulted in changes in their chemical composition. The antimicrobial activity of the tested oils was evaluated by determining the minimum inhibitory concentrations and zones of inhibition in agar. After ozonation, the acid content increased in all the tested oils. The highest acidity was found in linseed oil (13.00 ± 0.11 mg KOH/g; 6.1%). Hemp oil, whose acidity was also significant (second only to linseed oil), was the least acidified by ozonation (11.45 ± 0.09 mg KOH/g; 5.75%). After ozonation, the iodine value in oils was significantly reduced (45–93%), and the highest amounts of iodine value remained in linseed (47.50 ± 11.94 g Iodine/100 g oil) and hemp (44.77 ± 1.41 Iodine/100 g oil) oils. The highest number of peroxides after the ozonation of oils was found in sunflower oil (382 ± 9.8 meqO2/kg). It was found that ozonated hemp and linseed oils do not solidify and remain in liquid form when the temperature drops. The results showed a tendency for the reference strains of S. aureus, E. faecalis, and E. coli to have broader zones of inhibition (p < 0.001) than clinical strains. Overall, ozonated linseed oil had the highest antibacterial activity, and ozonated olive oil had the lowest, as determined by both methods. It was found that ozonated linseed oil was the most effective on bacteria, while the most sensitive were S. aureus ATCC 25923, MRSA, and S. pseudointermedius (MIC 13.5 mg/mL, 4.6 mg/mL, and 13.5 mg/mL, respectively, and sterile zones 20.67 ± 0.98 mm, 20.25 ± 0.45 mm, and 18.25 ± 0.45 mm, respectively). The aim and new aspect of this work is the characterisation of selected ozonated vegetable oils, especially hemp oil, according to chemical and antibacterial parameters, in order to select suitable candidates for preclinical and clinical animal studies in the treatment of bacterial or fungal skin infections in terms of safety and efficacy.