In this work, the adsorption of toluene on puresilica MEL zeolite is investigated using a variety of experimental and simulation methods. First, we measured the volumetric and calorimetric isotherms at 301 K and at 315 K. The volumetric adsorption isotherm presents a substep at a loading of roughly 4 molecules per unit cell that shifts to higher pressures at higher temperatures and that coincides with a sudden increase in the isosteric heat of adsorption. Grand canonical Monte Carlo simulations reveal that the substep at half load is caused by the adsorption of toluene molecules at different energetic sites within the porous network. According to this, toluene molecules occupy first the intersections, and once all intersections are filled, additional toluene molecules place themselves within the channels. The structure of the adsorbate/adsorbent system was further investigated by performing X-ray powder diffraction experiments of the zeolite at three different loads: empty, at half load (before the substep), and at high load (after the substep). Numerous new low intensity peaks and splittings of existing peaks at the empty and half-loaded diffractograms appear in the diffraction pattern of the high load sample. Atomic structural models compatible with the experimental spectra were obtained by performing N-reverse Monte Carlo simulations. Whereas at half load a good fit of the experimental diffraction pattern can be obtained using the rigid zeolite approximation, at high load, this is only possible when the flexibility of the zeolite is incorporated. In this structural model, the channel cross sections are deformed from a nearly circular shape in the empty zeolite to a more elliptical shape in the case of the high load zeolite.