We investigate hydrogen isotope and nuclear quantum effects on geometries and binding energies of small protonated rare gas clusters (Rg X , Rg = He,Ne,Ar, X = H,D,T, and = 1–3) with the any particle molecular orbital (APMO) MP2 level of theory (APMO/MP2). To gain insight on the impact of nuclear quantum effects on the different interactions present in the Rg X systems, we propose an APMO/MP2 energy decomposition analysis scheme. For RgH ions, isotopic substitution leads to an increase in the stability of the complex, because polarization and charge transfer contributions increase with the mass of the hydrogen. In the case of Rg H complexes, isotopic substitution results in a shortening and weakening of the rare gas-hydrogen ion bond. For Rg X complexes, the isotope effects on the rare gas binding energy are almost negligible. Nevertheless, our results reveal that subtle changes in the charge distribution of the Rg X core induced by an isotopic substitution have an impact on the geometry of the Rg X complex. © 2012 Wiley Periodicals, Inc.