Nanohybrids based on maghemite iron oxide nanoparticles (IONPs) and carbon dots (CDs), with different linkers between the two components, are synthesized, with the idea of combining several properties (magnetic and optical) in one nanomaterial in order to eradicate bacterial biofilm. The photothermal capacities of these materials are expressed by two parameters: the specific absorption rate (SAR) and the photothermal light-to-heat conversion constant (η). They show that the IONP/CD combination is more effective in photothermia (PT) than either of the components, but depends on the linkage (amide > ester > electrostatic). The antibacterial properties of the nanohybrids are first determined for the exponential and stationary growth phases of planktonic S. aureus and B. subtilis with and without PT. In the absence of PT, no nanohybrid has any significant bactericidal effect, but with PT the nanohybrids have different activities, with the IONP-amide-CD pattern the most effective. Combining magnetic actuation and PT on B. subtilis biofilms shows a synergistic effect and reveals the advantages of using such nanohybrid materials for killing bacteria and eradicating biofilm.