This study investigated the ability of Phyllanthus emblica encapsulated within chitosan-coated casein (CS-casein-Amla) nanoparticles to inhibit the growth of multi-drug-resistant Pseudomonas aeruginosa (P. aeruginosa) bacteria and prevent the formation of biofilms. The MDR strains underwent screening, and the morphological characteristics of the resulting nanoparticles were assessed using SEM, DLS, and FTIR. In addition, the efficacy of encapsulation, stability, and drug release were evaluated. The PpgL, BdlA, and GacA biofilm gene transcription quantities were quantified by quantitative real-time PCR. Simultaneously, the nanoparticles were assessed for their antibacterial and cytotoxic effects using the well diffusion and MTT procedures. CS-casein-Amla nanoparticles with a size of 500.73 ± 13 nm, encapsulation efficiency of 76.33 ± 0.81%, and stability for 60 days at 4 °C (Humidity 30%) were created. The biological analysis revealed that CS-casein-Amla nanoparticles exhibited strong antibacterial properties. This was shown by their capacity to markedly reduce the transcription of PpgL, BdlA, and GacA biofilm genes at a statistically significant value of p ≤ 0.01. The nanoparticles demonstrated decreased antibiotic resistance compared to unbound Amla and CS-casein. Compared to Amla, CS-casein-Amla nanoparticles showed very little toxicity against HDF cells at dosages ranging from 1.56 to 100 µg/mL (p ≤ 0.01). The results highlight the potential of CS-casein-Amla nanoparticles as a significant advancement in combating highly resistant P. aeruginosa. The powerful antibacterial properties of CS-casein-Amla nanoparticles against P. aeruginosa MDR strains, which are highly resistant pathogens of great concern, may catalyze the development of novel antibacterial research approaches.