Multidrug-resistant Acinetobacter baumannii is a well-documented pathogen associated with hospital-acquired infections. In addition to multidrug resistance, A. baumannii can also become resistant to colistin, the antibiotic treatment of last resort, by the loss of the lipopolysaccharide from its outer membrane. Here, we demonstrate that the development of colistin resistance also increases the resistance of A. baumannii to titanium dioxide (TiO2) photocatalysis. Both colistin-sensitive A. baumannii (CSAB) and colistin-resistant A. baumannii (CRAB) were inactivated by TiO2 when irradiated by ultraviolet A (UV-A). The resistance of CRAB to TiO2 photocatalysis was 1.5 times higher than that of CSAB, as determined by either culture assay or quantification of leaked proteins after photocatalysis (p < 0.05). The results of two-dimensional gel electrophoresis led to the speculation that the high resistance of CRAB may be associated with a lack of sensitive targets and oxidative enzymes. This hypothesis was confirmed by antimicrobial assays with 25 mM hydrogen peroxide (H2O2) and 1.07 mM sodium hypochlorite (NaClO). CRAB was significantly more resistant to H2O2 and NaClO treatment than CSAB (p < 0.01), consistent with the results of the TiO2 inactivation experiment. Therefore, the antibiotic resistance profiles of bacterial strains should be considered before the use of strains as indicators to represent sanitary quality after TiO2 photocatalysis.