Adsorption of five relevant low molecular weight polyphenols identified in agro-industrial waste extracts (Aristotelia chilensis leaves, Carménère wine pomace, spent coffee grounds, and brewery waste streams) was measured and characterized. SuperoseTM 12 prep grade and between three and six solutions with different water, ethanol, and acetic acid compositions were used as adsorbent and liquid phases. The chosen adsorbent and liquid phases were relevant for designing an adsorption preparative liquid chromatography (APLC) process to isolate these polyphenols. Langmuir and Freundlich models adequately fitted the obtained isothermal equilibrium data. The Freundlich model represented better ferulic acid (FA), kaempferol (KAE), and resveratrol (RSV) adsorptions, while the Langmuir model represented better gallic acid (GA) and catechin (CAT). Different polyphenol/agarose affinities in water-rich liquid phases were observed. From this, a hypothetical elution order was established (KAE < GA < FA < CAT < RSV), which was partially experimentally corroborated (for a mixture of GA, CAT, and RSV) with an APLC system. Lowering the water proportion or increasing the EtOH:HAc ratio in the liquid phase reduced the adsorption of these polyphenols, except for FA. The decrease in adsorption with temperature and the negative values of ΔH indicated that these processes were exothermic. The adsorption of all the polyphenols was governed by physisorption. All the adsorption processes studied were spontaneous and thermodynamically feasible (ΔG < 0). In addition, the polyphenol molecules were less randomly organized (more ordered) at the polyphenol/agarose interface during the adsorption process (ΔS < 0).