Exploitation of engineered nanomaterials with unique properties has been dynamically growing in numerous fields, including the agricultural sector. Due to the increasing resistance of phytopathogenic microbes, human control over various plant pathogens in crop production is a big challenge and requires the development of novel antimicrobial materials. Photocatalytic active nanomaterials could offer an alternative solution to suppress the plant pathogens. In this work, titanium dioxide nanoparticles (TiO2 NPs) with high photocatalytic activity were synthesized by hydrothermal post-treatment of amorphous titania at different temperatures (250 °C or 310 °C) without using any additives or doping agents. The obtained samples were investigated through X-ray diffraction, N2-sorption measurements, diffuse reflectance UV-Vis spectroscopy, transmission electron microscopy, electron paramagnetic resonance spectroscopy, and X-ray photoelectron spectroscopy. The applied hydrothermal treatment led to the formation of TiO2 nanocrystallites with a predominant anatase crystal phase, with increasing crystallinity and crystallite size by prolonging treatment time. The photocatalytic activity of the TiO2 NPs was tested for the photo-degradation of phenol and applied for the inactivation of various plant pathogens such as Erwinia amylovora, Xanthomonas arboricola pv. juglandis, Pseudomonas syringae pv. tomato and Allhorizobium vitis. The studied bacteria showed different susceptibilities; their living cell numbers were quickly and remarkably reduced by UV-A-irradiated TiO2 NPs. The effectiveness of the most active sample prepared at 310 °C was much higher than that of commercial P25 TiO2. We found that fine-tuning of the structural properties by modulating the time and temperature of the hydrothermal treatment influenced the photocatalytic properties of the TiO2 NPs considerably. This work provides valuable information to the development of TiO2-based antimicrobial photocatalysts.