A Ru(II)-based catalyst trapped within an amphiphilic, folded polymer is employed for the oxidation of secondary alcohols to their corresponding ketones using tBuOOH as the oxidant. Under the applied catalytic conditions, the polymer catalyst forms a compartmentalized structure with a hydrophobic interior. We selected secondary alcohols that differ in hydrophobicity, reactivity, and steric hindrance as substrates, with the aim to elucidate how this affects the rate and the end conversion of the oxidation reaction. Our investigations show that the Ru(II)-based catalyst is very efficient for oxidation reactions in water. Moreover, high selectivity toward the more hydrophobic substrate is observed, which originates from the hydrophobic interior of the compartmentalized catalyst system. This hydrophobic selectivity is also observed in the reverse reaction, the transfer hydrogenation.