The removal of carbon deposits from carburized Fe-based Fischer–Tropsch catalysts is a critical aspect of their performance. In this study, a method is presented to remove carbon deposits from freshly prepared χ-Fe5C2. The method involves successive passivation and reduction steps, which do not affect the bulk structure of the χ-Fe5C2 catalyst. The passivation step transforms the carbonaceous deposits from a graphitic structure to a disordered oxygen-functionalized structure, facilitating its removal by a reduction step in hydrogen. This results in a higher initial activity of the catalyst and substantially shortens the induction period observed without such pretreatment. The findings underscore the possibility of improving catalytic performance of Fe-carbides by changing the structure and reactivity of carbonaceous deposits.