Adsorption equilibria of alkane-α, ω-diols (propane-1,3-diol, butane-1,4-diol, pentane-1,5-diol, and hexane-1,6-diol) from aqueous solution onto an all-silica zeolite of the type mordenite framework inverted (MFI, also known as silicalite-1) are obtained by simulations and experiments at T = 323 K and also for pentane-1,5-diol (C5) at 348 and 383 K. After an initial slow rise, isotherms at T = 323 K exhibit steep changes in loading, reaching saturation at 10, 9, 8, and 7 molec/uc as the number of carbon atoms of the diols increases from 3 to 6. The abrupt change in loading corresponds to a minimum in the free energy of adsorption (from vapor to zeolite) that is associated with a rapid rise in the number of hydrogen bonds per sorbate molecule due to the formation of large clusters. For C5 at low loading, the centers-of-mass primarily occupy the channel intersections with oxygens oriented along the straight channels where intermolecular hydrogen bonds are formed. At saturation loading, the C5 centers-of-mass instead occupy the straight and zig-zag channels, and nearly all C5 molecules are involved in a percolating hydrogen-bonding network (this also occurs for C6). With increasing temperature, the C5 isotherm decreases in steepness as the minimum in free energy of adsorption decreases in depth and a less-ordered structure of the adsorbed molecules results in a lower number of diol–diol hydrogen bonds. However, the C5 isotherm does not shift significantly in concentration of the adsorption onset, as the free energies of solvation and adsorption increase by similar and compensating amounts. At T = 323 and 348 K, the steep change for the C5 adsorption isotherm is found to be a phase transition (as indicated by a bimodal distribution of unit cell occupancies at intermediate loading) from a less-dense phase with only small hydrogen-bonded clusters to an ordered solid phase with loadings of 8 molec/uc. At T = 383 K, the sorbates are less ordered, the distribution of occupancies becomes unimodal at intermediate loading, and the loading rises more gradually with concentration. Several different enhanced sampling methods are utilized for these simulations.