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Molecular surgery provides the opportunity to study relatively large molecules encapsulated within a fullerene cage. Here we determine the location of an H2O molecule isolated within an adsorbed buckminsterfullerene cage, and compare this to the intrafullerene position of HF. Using normal incidence X-ray standing wave (NIXSW) analysis, coupled with density functional theory and molecular dynamics simulations, we show that both H2O and HF are located at an off-centre position within the fullerene cage, caused by substantial intra-cage electrostatic fields generated by surface adsorption of the fullerene. The atomistic and electronic structure simulations also reveal significant internal rotational motion consistent with the NIXSW data. Despite this substantial intra-cage interaction, we find that neither HF or H2O contribute to the endofullerene frontier orbitals, confirming the chemical isolation of the encapsulated molecules. We also show that our experimental NIXSW measurements and theoretical data are best described by a mixed adsorption site model. The chemical nature of molecules encapsulated within fullerenes remain debated, with reports proposing a Faraday cage effect. Here, the authors show that H2O and HF molecules encapsulated inside a C60 cage experience a substantial intra-cage electrostatic interaction that results in off-center locations; despite this, the endofullerene’s frontier orbitals is unaffected, resulting in chemical shielding of the caged molecule.