Nucleobases such as guanine, xanthine, and uracil have been detected in numerous carbonaceous chondrites (CCs), with isotope signatures indicating their extraterrestrial origin. A correlation between nucleobase concentrations and the alteration degree of parent bodies is often reported, highlighting the importance of understanding the influence of aqueous alteration on nucleobase evolution to decode early solar system organic materials. Therefore, a laboratory investigation of the evolution of guanine, uracil, and xanthine was performed under aqueous alteration conditions typical of CCs. Given the intimate association of organic molecules with inorganic materials in CC matrices, we also included a set of inorganic phases in this study to discuss the influence of minerals on nucleobase evolution during aqueous alteration. Results showed that guanine and uracil exhibit high stability, while xanthine undergoes decarboxylation. Saponite traps about 25% of xanthine, 53% of uracil, and nearly all guanine, promoting nucleobase preservation. The isotope values (δ13C and δ15N) of nucleobases remained constant through aqueous alteration, suggesting that their isotope signatures are related to synthesis in cold environments in the proto solar nebula or the parent molecular cloud. The relative stability of guanine during aqueous alteration explains its abundance in meteorites. Nevertheless, other processes such as (geo)chromatographic effects may account for the observed decrease in guanine abundance with the increasing degree of alteration in CCs. The reported concentrations of uracil and xanthine in CCs are not correlated with the alteration degree; hence, differences in relative abundance are either related to different parent body reservoirs or synthesis/migration during aqueous alteration events.