A novel method for the electrochemical template synthesis of surface-imprinted magnetic polymer microrods for protein recognition is proposed. The polymer was electrodeposited into sacrificial cylindrical microreactors, the internal walls of which were previously modified with a target model protein, avidin, by simple physisorption. The electropolymerization was performed from a mixture of 3,4-ethylenedioxythiophene, poly(styrenesulfonate) (PSS), and PSS-coated superparamagnetic nanoparticles resulting in the formation of inherently electroconductive polymers confined to the volume of the microreactor. Here we show that: (i) the template synthesis within cylindrical microreactors results in polymer rods with dimensions matching that of the reactor, (ii) the incorporation of superparamagnetic particles induces magnetic properties that allow for efficient collection and manipulation of the microrods released from the microreactors in magnetic field even from dilute solution, and (iii) the protein coating on the internal walls of the microreactors is shown to generate molecular imprints on the surface of the polymeric rods. This latter property was demonstrated by comparative binding experiments of a fluorescent avidin derivative to the surface-imprinted and non-imprinted magnetic polymer microrods.