This manuscript reports a comparative study of the catalytic performance of gold nanoparticles (NPs) encapsulated within MIL-101(Cr) with or without amino groups in the terephthalate linker. The purpose is to show how the amino groups can influence the microenvironment and catalytic stability of incorporated gold nanoparticles. The first influence of the presence of this substituent is the smaller particle size of Au NPs hosted in MIL-101(Cr)-NH2 (2.45±0.19 nm) compared with the parent MIL-101(Cr)-H (3.02±0.39 nm). Both materials are highly active to promote the aerobic alcohol oxidation and exhibit a wide substrate scope. Although both catalysts can achieve turnover numbers as high as 106 for the solvent-free aerobic oxidation of benzyl alcohol, Au@MIL-101(Cr)-NH2 exhibits higher turnover frequency values (12 000 h−1) than Au@MIL-101(Cr)-H (6800 h−1). Au@MIL-101(Cr)-NH2 also exhibits higher catalytic stability, being recyclable for 20 times with coincident temporal conversion profiles, in comparison with some decay observed in the parent Au@MIL-101(Cr)-H. Characterization by transmission electron microscopy of the 20-times used samples shows a very minor particle size increase in the case of Au@MIL-101(Cr)-NH2 (2.97±0.27 nm) in comparison with the Au@MIL-101(Cr)-H analog (5.32±0.72 nm). The data presented show the potential of better control of the microenvironment to improve the performance of encapsulated Au nanoparticles.