The global spread of antibiotic-resistant strains, and the need to protect the microflora from non-specific antibiotics require more effective and selective alternatives. In this work, we demonstrate for the first time a superior antibacterial photothermal effect of plasmonic gold nanorods (AuNRs) via their incorporation onto natural clay halloysite nanotubes (HNTs), which were functionalized with anti-E. coli antibodies (Ab-HNTs). AuNRs were incorporated onto the Ab-HNTs through a facile freeze–thaw cycle, and antibody integrity following the incorporation was confirmed via infrared spectroscopy and fluorescence immunolabeling. The incorporation efficiency was studied using UV-Vis absorption and transmission electron microscopy (TEM). Mixtures of E. coli and AuNR-Ab-HNTs hybrids or free AuNRs were irradiated with an 808 nm laser at 3–4 W cm−2, and the resulting photothermal antibacterial activity was measured via plate count. The irradiated AuNR-Ab-HNTs hybrids exerted an 8-fold higher antibacterial effect compared to free AuNR under 3.5 W cm−2; whereas the latter induced a 6 °C-higher temperature elevation. No significant antibacterial activity was observed for the AuNR-Ab-HNTs hybrid against non-target bacteria species (Serratia marcescens and Staphylococcus epidermidis). These findings are ascribed to the localization of the photothermal ablation due to the binding of the antibody-functionalized clay to its target bacteria, as supported through TEM imaging. In the future, the HNTs-based selective carriers presented herein could be tailored with other antibacterial nanoparticles or against another microorganism via the facile adjustment of the immobilized antibody.