Particle-based photodynamic therapy (PPDT) holds great promise in theranostic applications. Herein, we demonstrate that PPDT based on gold nanorods coated with an indocyanine green (ICG)-loaded silica shell allows for the inactivation of the Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 (E. coli LF82) under pulsed laser light irradiation at 810 nm. Fine-tuning of the plasmonic structures together with maximizing the photosensitizer loading onto the nanostructures allowed optimizing the singlet oxygen generation capability and the PPDT efficiency. Using a nanoparticle concentration low enough to suppress photothermal heating effects, 6 log10 reduction in E. coli LF82 viability could be achieved using gold nanostructures displaying a plasmonic band at 900 nm. An additional modality of nanoparticle-based photoinactivation of E. coli is partly observed, with 3 log10 reduction of bacterial viability using Au NRs@SiO2 without ICG, due to the two-photon induced formation of reactive oxygen species. Interaction of the particles with the bacterial surface, responsible for the disruption of the bacterial integrity, together with the generation of moderate quantities of singlet oxygen could account for this behavior.