This study investigates the effect of co-doping with nanographene on the properties of FTO layers produced by spray pyrolysis. The results show that co-doping with nanographene enhances phase separation processes within the bulk of the FTO layer. The inhomogeneities formed during phase separation are depleted of fluorine compared to the film bulk. Co-doping with nanographene also significantly modifies the optical properties of the FTO layers. Specifically, it alters the position and intensity of the peaks in the reflection spectra, indicating a change in the nature of the absorbing centers. Furthermore, the optical bandgap of the FTO layers decreases with an increasing degree of nanographene doping. Finally, co-doping with nanographene reduces the resistance of the FTO layers, which can be attributed to an increase in charge carrier mobility.