The cathodic deposition of iron–cobalt alloys inside the pores of anodically formed nanoporous silicon (PS) from p-type Si substrate is investigated with respect to the electrolyte composition. The samples were characterized by scanning electron microscopy, energy dispersive spectrometry, Auger electron spectroscopy, and Fourier transform infrared spectroscopy. Results showed that the nucleation of pure cobalt started at the bottom of the pores and the nucleation of pure iron occurred all over the pore walls, leading to a preferential deposition on top surface of the porous layer. Nevertheless, a low concentration of Co2+ ions (5 at.%) in the electrolyte drastically improved the penetration of iron into the pores. As a result, a good filling of the pores with Co metal as well as with Fe–Co alloys was achieved. It was also shown that the deposition process oxidizes the structure mainly at the pore walls. The results of our investigation indicate that the mechanisms occurring during the electrodeposition of metals on porous p-type silicon substrates are completely different depending on the kind of electrolyte used: pure iron-based electrolyte or cobalt-based solutions. A complete understanding of the deposition process requires further analyses of the carrier transport in PS and of the charge exchange at the Si/electrolyte and PS/electrolyte interfaces. These new results involving the deposition of iron-group materials into porous p-type silicon are useful for future silicon technologies.