Nanoparticles (NPs) of cobalt are synthesized in shallow layers of polyimide using 40 keV implantation of Co+ ions with a few different fluences at various ion current densities. Nucleation of individual NPs at low fluencies and their percolation at high fluencies are crucial processes governing the electrical and magnetic properties of the metal/polymer nanocomposites that can be controlled by the implantation regimes. In particular, one can tune the magnetoresistance between negative and positive through appropriate choice of ion fluence and current density. The found non-monotonous dependence of the magnetoresistance on the applied magnetic field allows suggestion of spin-dependent domain wall scattering affecting the electron transport. The samples implanted with low fluencies demonstrate superparamagnetic behavior down to very low blocking temperatures. For high fluence (1.25 × 1017 cm−2) the transition to ferromagnetic ordering is observed that is related to the increased magnetic interaction of NPs.