The microstructural changes induced by ion implantation may lead to advantageous modifications of chromium disilicide's (CrSi2) electrical and thermal properties. As a potential thermoelectric material, CrSi2 has attracted attention due to its semiconductor properties and high thermal stability. This contribution investigates the influence of different ion species and implantation conditions on the microstructure, electrical resistivity ρ and thermal conductivity κ behaviors in amorphous CrSi2 thin films. ~ 260-nm-thick CrSi2 films were produced by magnetron sputtering and deposited onto a SiO2/Si substrate. Samples were implanted at room temperature either with Ne or Al ions to form a concentration–depth plateau reaching a concentration of ≈ 1.0 at.% (Ne), or ≈ 0.008 at.% (Al). Ne and Al implantations were also performed with the targets heated at 250 °C. The microstructural modifications were characterized via TEM and STEM-EDX. The electrical resistivity ρ was measured by the van der Pauw method, and the thermal conductivity κ measurements were obtained with SThM. The results obtained show that room temperature Al and Ne implantations cause the reduction of ρ as compared to the pristine film. In contrast, the ρ values are significantly higher for Ne and Al implantations in heated substrates. The microstructure evolution, electrical and thermal behaviors are discussed considering the effects of radiation damage and the formation of dense nanocrystallite arrays during the implantation process.