This study aims to explore the antimicrobial activity of rifampicin (RIF) and ascorbic acid (ASC) co-loaded into alginate (ALG)/chitosan (CS) nanoparticles (RIF/ASC NPs) and tested for their antibacterial activity against several strains of methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). Also, the present research focused on exploring the possible antibacterial mechanism of action of these RIF/ASC NPs, which demonstrated a significant biocide activity against the S. aureus strains with minimum inhibitory concentrations (MIC) between 2- and 8-fold lower than those one exhibited with the free antibiotic RIF. The proposed antimicrobial mechanism of action of the RIF/ASC NPs seems to be the result of collaborative effects between NPs and the RIF/ASC antibiotic combination. Moreover, results indicated that the functionalized RIF/ASC NP surface played a crucial role on the processes of NP adhesion into the bacterial surface, the alterations on the cell membrane integrity, and the cell uptake of the RIF/ASC antibiotic into bacteria. Further, the in vivo lung deposition pattern of empty NPs labeled (NPs-FITC) with isothiocyanate fluorescein in rats was investigated post intratracheal instillation of NPs. In summary, findings from this work show that our novel designed engineered RIF/ASC co-loaded NPs could be a suitable system for antibiotic lung administration with promising perspectives for effective treatments of pulmonary intracellular infections for those known antibiotics that are losing effectiveness due to antimicrobial resistance problems. Graphical Abstract.