Vertically oriented and ferrocene functionalized mesoporous silica thin films have been prepared by combining the electrochemically assisted self-assembly (EASA) method with click chemistry. The resulting films are electroactive, involving an electron hopping mechanism between adjacent ferrocene moieties. The electrochemical oxidation of ferrocene into ferricinium ion generates positive charges that are compensated by the ingress of anions into the film, opening the door to possible indirect amperometric detection of non-electroactive anions by flow injection analysis. Operating in an electrolyte-free flow, each injection of an anion (e.g., NO3−) at an electrode biased at a suitable positive potential (i.e., +0.5 V) gave rise to an amperometric response proportional to the anion concentration. However, to avoid the decrease of the electrochemical signal due to the progressive consumption of ferrocene in multiple successive analyses, it was necessary to regenerate the electrode by reduction of ferricinium moieties, which can be achieved in-situ by square wave amperometry. The feasibility to apply such indirect amperometric detection scheme in suppressed ion chromatography (for detecting anions in mixture) was also demonstrated.