The mobile phases employed in current practice of supercritical fluid chromatography (SFC) are usually composed of a mixture of pressurized carbon dioxide and a co-solvent. The co-solvent is most often an alcohol and may contain a third component in small proportions, called an additive (acid, base or salt). In the first part of this series, the effects of mobile phase additives on the polarity and apparent pH of the mobile phase were explored. In the present paper, we examine the effects pertaining to adsorption of additives on the stationary phase. Ammonium acetate was selected as a representative case, because it is often employed in current practice. To favour its solubility and further improve chromatographic quality, a small portion of water is also advocated. First, the equilibration time is observed to be largely increased in the presence of an additive, especially when mobile phase compositions containing only low proportions of methanol co-solvent are employed. Secondly, the effects of ammonium acetate are more thoroughly assessed with a modified version of the solvation parameter model (five Abraham descriptors and two descriptors to take account of positive and negative charges on ionizable species). On a hybrid silica stationary phase (ACQUITY UPC2 BEH), the effects of increasing concentration of ammonium acetate (0-25 mM in the methanol co-solvent) are investigated. The retention of acidic species is the most strongly affected, with a continuous retention increase when additive concentration increases. The retention of basic and neutral species is also moderately affected. Then thirty-two stationary phases based on sub-2 μm totally porous particles or sub-3 μm superficially porous particles are characterized with and without 20 mM ammonium acetate and 2% water in the methanol co-solvent. The effects of adsorbed additive on the interaction capabilities are discussed. Finally, the interest of introducing the additive in the dilution solvent, a method that was sometimes recommended to simplify the workflow, is also discussed with a model basic compound.