Intercalation and doping are promising routes to tune properties of van der Waals (vdW) semiconductors and pave the way for their applications in digital electronics beyond Moore’s law, sensors and spintronics. The indium selenide (InSe) vdW crystal shows great promise for use in next-generation semiconductor technologies. For these applications to be realized, the effects of impurities on properties of InSe must be understood. Here, we present a comparative experimental study of electron transport in n-type InSe semiconductor doped and electrochemically intercalated with magnetic cobalt (Co) impurities. It is shown that the presence of Co decreases the free electron density, the Hall mobility along layers and the conductivity anisotropy σ^С/σ||С. Furthermore, this leads to a change of the behavior of σ^С(Т) dependence from a metallic one in pristine samples to a semiconducting one in samples with Co. We also demonstrate that the interaction of electrons with space-charge regions is an effective scattering mechanism, which should be taken into account in doped and intercalated crystals. The present work is important for the basic physics knowledge of the effect of Co impurities on physical properties of InSe, which is needed to tailor the parameters of this semiconductor for applications in electronics and spintronics.