Polyelectrolyte multilayer capsule reactors (PEMCRs) for the synthesis of two types of nanoparticles were prepared. The tunable PEMCRs containing two different functional groups that can be used to synthesize two types of nanoparticles simultaneously and to control the composition of two types of nanoparticles within the shell of PEMCs. These PEMCRs enabled the composition as well as the amount of the loaded two types of nanoparticles within the shell of PEMCs to be controlled by the copolymer ratio and the number of reaction cycles. Another interesting finding is that, as a result of the synthesis of two types of nanoparticles, these specially designed PEMCs containing both silver and goethite nanocrystals can be used as antimicrobial capsules, which can move by an external magnetic field. Such a technology has the potential for use in sterilization at the desirable sites.