It is demonstrated here that bioactive glasses containing Au nanoparticles (AuNPs) can be selectively functionalized with small molecules carrying either amino or thiol groups by simply varying the temperature and pH of the functionalization batch. The results evidence the following. (i) At room temperature (RT), no functionalization of Au-free glass occurs, whereas in the case of glasses containing AuNPs, stable linkages form only with amino groups, as in this condition Au does not bind with either thiol or hydroxyl groups. The RT functionalization with cysteine and cystine confirms the preferential functionalization through the amino groups, while the -SH groups are oxidized to S-S bridges. (ii) The functionalization with cysteine and cystine, compared at pH = 5, 9, and 12, is shown not to take place at pH = 5 and to be hindered by the glass matrix dissolution at pH = 12 (with consequent release of AuNPs), while the best results are obtained at pH = 9. (iii) For the effect of reaction temperature, at 4 °C it is possible to obtain a strong Au-S interaction, whereas at RT, a weak Au-N linkage is formed. These results should allow production, in a selective way, of different bonds exhibiting different strengths and, consequently, different release times in solution, with a wide range of possible applications (for instance, weak Au-N bonds in the case of drug delivery, strong Au-S bonds in protein immobilization).