The aim of this work was to evaluate the effect of different inorganic compounds as electron donors for the capture of CO2 from a model cement flue gas CO2/O2/N2 (4.2:13.5:82.3% v/v) using a non‐photosynthetic microbial community. The inoculum obtained from a H2‐producing reactor was acclimated to CO2 consumption achieving 100% of CO2 removal after 45 days. Na2S, MnCl2, NaNO2, NH4Cl, Na2S2O3, and FeCl2 were used as energy source for CO2 fixation by the acclimated microbial community showing different efficiencies, being Na2S the best electron donor evaluated (100% of CO2 consumption) and FeCl2 the less effective (28% of CO2 consumption). In all treatments, acetate and propionate were the main endpoint metabolites. Moreover, scaling the process to a continuous laboratory biotrickling filter using Na2S as energy source showed a CO2 consumption of up to 77%. Analysis of the microbial community showed that Na2S and FeCl2 exerted a strong selection on the microbial members in the community showing significant differences (PERMANOVA, p = 0.0001) compared to the control and the other treatments. Results suggest that the CO2 fixing pathways used by the microbial community in all treatments were the 3‐hydroxypropionate‐4‐hydroxybutyrate cycle and the Wood‐Ljungdahl pathway.