Bacteria in biofilms are much more resistant to antibiotics and microbicides as compared to their planktonic stage. Thus, to achieve the same antibacterial efficacy, a much higher dose of antibiotics is required for biofilm bacteria. However, the widespread use of antibiotics has been recognized as the main cause for the emergence of antibiotic-resistant microbial species, which has now become a major public health crisis globally. In this work, we present an efficient nonantibiotic-based strategy for disrupting biofilms using carboxymethyl chitosan (CMCS) coated on magnetic iron oxide nanoparticles (CMCS-MNPs). CMCS-MNPs demonstrate strong bactericidal activities against both Gram-positive Staphylococcus aureus (S. aureus) and Gram-negative Escherichia coli (E. coli) planktonic cells. More than 99% S. aureus and E. coli planktonic cells were killed after incubation with CMCS-MNPs for 10 and 5 h, respectively. In the presence of a magnetic field (MF), CMCS-MNPs can effectively penetrate into both S. aureus and E. coli biofilms, resulting in a reduction of viable cells counts by 84% and 95%, respectively, after 48 h incubation, as compared to the control experiment without CMCS-MNPs or CMCS. CMCS-MNPs are noncytotoxic toward mammalian cells and can potentially be a useful antimicrobial agent to eliminate both planktonic and biofilm bacteria.