Cerium-doped mixed garnet-type single crystals (GdxY1-x)3Al2Ga3O12 with different yttrium content have been fabricated and studied as a prospective scintillating material enabling improvement of scintillation properties by tuning the composition of the matrix-building crystal. The influence of the matrix composition on the emitting Ce ion is studied using linear and time-resolved nonlinear optical absorption and time-resolved photoluminescence spectroscopy. The study of photoluminescence at resonant excitation revealed a composite origin of Ce3+ emission band. This behavior is interpreted by the contribution of Ce3+ ions located in inequivalent positions expected due to the disorder caused in the garnet-type lattice of a mixed crystal by compositional fluctuations. The substitution of gadolinium by yttrium in the lattice results not only in an emission blue shift and in decreased splitting of the lowest doublet 5d state of Ce3+ but also in an increased separation between the lowest doublet level 5d1 and the lowest triplet 5d3 level, as well as in changing the rates of intracenter and extracenter energy relaxation. Display omitted •Photoluminescence spectrum is composite due to inequivalent positions of Ce3+ ions.•Decay time of Ce3+ emission decreases from 55 ns at 1.9 eV to 40 ns at 2.5 eV.•Substitution of Gd by Y decreases 5d1-5d2 splitting of Ce3+ and increases 5d1-5d3 separation.•Introduction of Y in GAGG lattice increases Ce3+ intracenter relaxation time.•Capture of trapped electrons to nonradiative recombination centers is enhanced in GYAGG.