The bacterial diversity retained in Al/Fe-pillared interlayered clay and Fe-functionalized granular activated carbon absorbent was characterized after their saturation with mature landfill leachate either before and after a tertiary, catalytic wet peroxide oxidation treatment. The 454 pyrosequencing analyses showed bacteria belonging to Phyla: Proteobacteria, Bacteroidetes and Actinobacteria. Flavobacterium was the most representative genus detected in three out of four studied adsorbents: the pillared clay before the catalytic oxidation and the granular activated carbon at both stages before and after the catalytic oxidation, whereas Haliscomenobacter, Rhodococcus Pseudomonas, Thermomonas, Aequorivita, and Acidovorax, were also found according to the type of absorbent. It was demonstrated the efficiency of the oxidizing treatment in the elimination of the immobilized leachate’s microorganisms when in the presence of the Al/Fe-pillared clay adsorbent; this exhibited the highest catalytic response, since no DNA was detected on this material after its catalytic treatment. Only in the case of the functionalized activated carbon, it was found the presence of microorganisms of environmental interest after the advanced oxidation stage. Although the bacterial community detected in the activated carbon after oxidizing treatment showed lower voltage output than that one before oxidation, such resistant bacteria could be potentially useful driving microbial fuel cells for degradation of more complex and harmful substrates. Thus, further studies should be done assessing the degradation of toxic and hazardous substances by microbial fuel cells in the presence of catalytic wet peroxide oxidation- and other advanced oxidation-resistant bacteria, including contaminants of emerging concern widely spread in wastewaters.