Charge ordering creates a spontaneous array of differently charged ions and is associated with electronic phenomena such as superconductivity, colossal magnetoresistances (CMR), and multiferroicity. Charge orders are usually suppressed by chemical doping and site selective doping of a charge ordered array has not previously been demonstrated. Here we show that selective oxidation of one out of eight distinct Fe2+ sites occurs within the complex Fe2+/Fe3+ ordered structure of 2%-doped magnetite (Fe3O4), while the rest of the charge and orbitally ordered network remains intact. This ‘charge order within a charge order’ is attributed to the relative instability of the trimeron distortion surrounding the selected site. Our discovery suggests that similar complex charge ordered arrays could be used to provide surface sites for selective redox reactions, or for storing information by doping specific sites.