The effect of proton irradiation with a dose of 50 Mrad (Si) on the optical properties and defect formation in crystals of gadolinium–aluminum–gallium garnet is studied during the substitution of aluminum and gallium in the cation sublattice: Gd3Al2Ga3O12 (Al : Ga = 2 : 3) and Gd3Al3Ga2O12 (Al : Ga = 3 : 2). After irradiation with protons, the crystals change color: an additional absorption band appears in the spectrum of each crystal in the wavelength range of 400–500 nm. This is due to the formation of induced structural defects in the form of color centers. The refractive indices n(λ) are determined by the Brewster spectrophotometric method and barely change for Al : Ga = 2 : 3 crystals, but largely increase for Al : Ga = 3 : 2. In the spectral dependences, there is a noticeable increase in the attenuation of light, which also indicates the formation of additional structural defects.