In this study, mesoporous silica nanoparticles (MSPs) of different size and shape were developed, and their surface coatings were utilized to study their differential effects in enhancing antibacterial activity. In brief, MSPs with three different aspect ratios (1, 2 and 4) were prepared, doped with silver ions and finally coated with the polymer chitosan. Both Gram-positive and Gram-negative bacteria were treated with the MSPs. Results indicate that silver ion doped and chitosan coated MSPs with the aspect ratio of 4 (Cht/MSP4:Ag+) have the highest antimicrobial activity among the prepared series. Further studies revealed that Cht/MSP4:Ag+ was most effective against Escherichia coli (E.coli) and least effective against Vibrio cholerae (V. cholerae). To investigate the detailed inhibition mechanism of the MSPs, the interaction of the nanoparticles with E.coli membranes and its intracellular DNA was assessed using various spectroscopic and imaging-based techniques. Furthermore, to increase the efficiency of the MSPs, a combinatorial antibacterial strategy was also explored, where nanoparticles, in combination with kanamycin (antibiotic), were used against Vibrio Cholerae (V. cholerae). Toxicity screening of these on MSPs was conducted on Caco-2 cells, and the results show that the dose used for antibacterial screening is below the limit of the toxicity threshold. Our findings show that both shape and surface engineering contribute positively towards killing bacteria, and the newly developed silver ion-doped and chitosan-coated MSPs have good potential as antimicrobial nanomaterials.