In the present contribution, columns packed with fully porous widepore 1.7 m particles (AcquitBEH300) and widepore core–shell 3.6 m particles (Aeris WP) were evaluated for the separation of model and therapeutic proteins of varying sizes, hydrophobicity and isoelectric points. Two types of bondin were compared, namely C4 and C18 in a systematic way. The kinetic performance of these stationary phases was evaluated in a previous paper hence this new work focuses on their retention behaviour, loading capacity and selectivity. Using the Tanaka tests, model proteins, and other confirmatory experiments, it is highly probable that with proteins, strong interaction mechanisms were predominant on the Aeris WP while the hydrophobic interaction was the driving force of the retention on the Acquity BEH300 material. This explained why, despite the lower pore volume of the Aeris WP material, the apparent retention factors of proteins possessing both hydrophobic and charged amino acids residues were very close on the four investigated columns. In terms of peak widths, values for proteins were similar for all the tested stationary phases, despite the probable strong ion exchange mechanisms of Aeris WP column. This could be explained by the excellent mass transfer characteristics afforded by the thin porous layer (∼0.2 m) at the surface of the particle which probably compensates for the slow secondary ionic interaction kinetics. The loading capacity was also evaluated on all the four widepore columns, using model proteins. On average, approximately 2–4 times higher amount of proteins can be injected on the fully porous BEH300 compared to the core–shell Aeris WP columns when avoiding 10% change in peak width or in tailing. However, this result could be strongly influenced by the nature and shape of the protein, its hydrophobicity, folding, size and number of charges. Finally, all of these columns were employed for the highly efficient separation of a therapeutic protein (interferon-2A) and some closely related proteins and showed excellent performance and selectivity. This result confirms that RPLC gained interest in the biopharmaceutical field as it provides significantly better peak widths than size-exclusion or ion-exchange and inherent compatibility with MS.