Herein, a facile approach toward converting a three-dimensional polyurethane sponge (PUS), employed in endoluminal vacuum-assisted closure (endo-VAC) therapies, in a theranostic material able to detect and to inhibit bacteria growth, has been reported. The endo-VAC PUS presented sensitivity to Gram-positive and Gram-negative bacterial species thanks to its functionalization with gold and silver antibacterial nanoparticles (NPs). PUS with chitosan-stabilized Au-NPs achieved 5.26 ± 0.17 logs and 2.78 ± 0.34 logs of reduction of bacteria growth, whereas the sponges functionalized with phenolated lignin Ag-NPs offered slightly inferior values (4.77 ± 0.36 logs and 2.03 ± 0.37 logs, respectively), against Escherichia coli and Staphylococcus aureus pathogens, respectively, after the application of photothermal ablation. The in vitro antimicrobial studies were contrasted with the in-situ monitoring of bacteria localization and inactivation with excitation lasers of 532 and 785 nm wavelengths, respectively, in the Raman equipment. The novel theranostic nano-enabled antimicrobial PU sponges offer unprecedented possibilities for the improvement of the endo-VAC treatments and extrapolation of the methodology to other plastic-based implants to combat antimicrobial resistances.