Formation of complex polyaniline (PANI) films with diamagnetic TCNQ and paramagnetic metal ion impurities cast under applied magnetic field was studied. It has been found that the applied magnetic field affects interaction of PANI chains with the impurities and induces formation of magnetically ordered regions in the complex film doped by paramagnetic metal ions in contrast to the reference film of the same composition but prepared under ambient conditions. The magnetically ordered regions have been observed directly by scanning magnetic force microscopy. It was found a correlation in distribution of the magnetically ordered regions and peculiarities of the surface relief of a film. Electronic absorption spectra and conductivity measurements showed that an applied stationary magnetic field can suppress the interaction of PANI chains and paramagnetic metal ions and lowers conductivity of the resulting complex film up to one order of magnitude as compared with the reference film. An alternating magnetic field was found to improve interaction of PANI and diamagnetic TCNQ molecules. The mechanisms of the magnetic field influence on the complex film formation are discussed.