Biofilms are the reason for a vast majority of chronic inflammation cases and most acute inflammation. The treatment of biofilms still is a complicated task due to the low efficiency of drug delivery and high resistivity of the involved bacteria to harmful factors. Here we describe a magnetically controlled nanocomposite with a stimuli-responsive release profile based on calcium carbonate and magnetite with an encapsulated antibiotic (ciprofloxacin) that can be used to solve this problem. The material magnetic properties allowed targeted delivery, accumulation, and penetration of the composite in the biofilm, as well as the rapid triggered release of the entrapped antibiotic. Under the influence of an RF magnetic field with a frequency of 210 kHz, the composite underwent a phase transition from vaterite into calcite and promoted the release of ciprofloxacin. The effectiveness of the composite was tested against formed biofilms of E. coli and S. aureus and showed a 71% reduction in E. coli biofilm biomass and an 85% reduction in S. aureus biofilms. The efficiency of the composite with entrapped ciprofloxacin was higher than for the free antibiotic in the same concentration, up to 72%. The developed composite is a promising material for the treatment of biofilm-associated inflammations.