The food of animal origin that is the most consumed is the table egg, but laying hens treated with antibiotics can produce eggs contaminated with antibiotic residues. Residues of antibiotics may present a risk for consumer health. Keeping in mind that laying hens almost always suffer from Mycoplasma (Mycoplasma synoviae), for which they are treated with antibiotics, high-quality egg production is even harder. Our research aimed to investigate the influence of three different antibiotics compared to the tea tree (Melaleuca alternifolia) essential oil administered to naturally infected laying hens with M. synoviae, on antibiotic residues in eggs as well as the egg nutritive and sensory qualities. A total of 20,000 laying hens, housed in one facility and divided into four lines each consisting of 5000 hens naturally infected with M. synoviae, was used. For the antimicrobial therapy, tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) were used, respectively. As a control, tea tree essential oil (TT) was used. Based on the gained results all tetracyclines treatment residue values were significantly (p < 0.05) higher compared to the control treatment (TT), but without any significant differences (p > 0.05) between themselves. The results showed no differences in the nutritive and the sensory qualities of eggs between the control and the experimental treatments (p > 0.05). Keeping in mind the obtained results from this study, it can be concluded that tea tree essential oil could be successfully used as a natural antibiotic in the treatment of M. synoviae, without any adverse effects on table egg quality.