Tuning the magnetic behavior of nanoparticles via the control of their features has always been challenging because these features are mostly intertwined. In the last years, a novel synthetic approach based on cation-exchange has been reported, and one of its main advantages is to maintain the shape and size of nanoparticles. However, such a synthetic strategy has been seldom applied to iron oxide magnetic nanoparticles, where the substitution of iron with diverse transition element cations was described as occurring in their whole volume. Surprisingly, we found results quite discordant from the few ones so far published in exploiting again this approach. We show here that it unavoidably leads to core/shell structures with only the shell undergoing the cation-exchange. Moreover, the starting phase of iron oxide strongly dictates the number of iron cations that could be replaced: if it is structurally free of vacancies, like magnetite, the maximum amount of exchanged cations is low and only affects the nanoparticles most external, disordered layers. Conversely, the cation-exchange is boosted if the iron oxide phase is structurally prone to vacancies, like wustite, and the shell where the iron cations have been partly substituted becomes quite thicker. These findings are further corroborated by the materials magnetic properties.