The effects of 10 MeV Al4+ ions irradiation on structural, surface morphological, optical and electrical properties of fluorine-doped tin oxide (FTO) substrates are presented for solar cell applications. The ions irradiation changes the surface morphology, average roughness, interface width, roughness exponent, and several other fractal parameters of the FTO surfaces. The UV–visible transmittance measurement shows an enhancement of transmittance in the ions irradiated substrates up to 95%. The electrical properties such as mobility, work-function, sheet resistance, and resistivity are also modified due to ions irradiation. In order to have functional applications of these ions irradiated substrates, we fabricated organic solar cells on these ions irradiated and pristine FTO substrates. The device performances are significantly improved for the case of ions irradiated FTO substrate in comparison to the pristine one. Thus, better device performance due to effective changes in physical properties suggests that the ions irradiated FTO substrates can be used as better electrodes for organic and hybrid photovoltaic device applications.