Many of the potential applications for metal-organic framework (MOF) materials require molecular level understanding of their adsorption of small organic molecules, which are not readily accessible from experiment. Through high-level van der Waals corrected, hybrid density functional theory calculations, we elucidate the adsorption configurations of several, representative small organic guest molecules in an archetypal flexible MOF material, MIL-53-Fe. The predicted relative energies between low-energy adsorption configurations of 1,4-benzoquinone in MIL-53-Fe are in very good agreement with the thermal transition temperatures observed experimentally and suggest thermodynamic factors govern the precise arrangements and loading of guests in the MOF host. Experimentally observed conformational disorder of small organic molecules in MIL-53-Fe is explained by predicted multiple low-energy adsorption configurations that are comparable with the thermal energy of the guests, kT. Finally, we show that the previously observed selective adsorption of pyridine and 2,6-lutidine molecules over water by MIL-53-Fe, can be rationalised through a careful analysis of the hostguest and guest-guest interactions and is controlled by thermodynamic factors.