We investigate hydrogen isotope and nuclear quantum effects on geometries and binding energies of small protonated rare gas clusters (Rg
$_n$X
$^ +$, Rg = He,Ne,Ar, X = H,D,T, and
$n$ = 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
$_n$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
$_2$H
$^ +$ complexes, isotopic substitution results in a shortening and weakening of the rare gas‐hydrogen ion bond. For Rg
$_3$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
$_2$X
$^ +$ core induced by an isotopic substitution have an impact on the geometry of the Rg
$_3$X
$^ +$ complex. © 2012 Wiley Periodicals, Inc.