The effect of various cleaning methods on coating morphology and their effectiveness in removing organic contaminants has been studied in this research. Bioactive coatings containing titanium oxides and hydroxyapatite (HAP) were obtained through plasma electrolytic oxidation in aqueous electrolytes and molten salts. The cleaning procedure for the coated surface was performed using autoclave (A), ultraviolet light (UV), radio frequency (RF), air plasma (P), and UV-ozone cleaner (O). The samples were characterized using scanning electron microscopy (SEM) with an EDS detector, X-ray photoelectron spectroscopy (XPS), X-ray phase analysis (XRD), and contact angle (CA) measurements. The conducted studies revealed that the samples obtained from molten salt exhibited a finer crystalline structure morphology (275 nm) compared to those obtained from aqueous electrolytes (350 nm). After applying surface cleaning methods, the carbon content decreased from 5.21 at.% to 0.11 at.% (XPS), which directly corresponds to a reduction in organic contaminations and a decrease in the contact angle as follows: A > UV > P > O. This holds true for both coatings obtained in molten salt (25.3° > 19.5° > 10.5° > 7.5°) and coatings obtained in aqueous electrolytes (35.2° > 28.3° > 26.1° > 16.6°). The most effective and moderate cleaning method is ozone treatment.