Microbial reduction of Fe(III) in clay minerals is an important process that affects properties of clay-rich materials and iron biogeochemical cycling in natural environments. Therefore the iron redox cycling in clay minerals is indirectly related to key environmental processes such as nutrient cycling, plant growth, contaminant migration, organic matter maturation and petroleum production. Fe(III) reduction experiments performed with a common ground water bacterium Shewanella putrefaciens CN32 in several clay minerals have found that the extent of Fe(III) reduction is qualitatively consistent with the difference in the crystal structure and layer charge of minerals with ferruginous nontronite being most reactive. Among Fe(III) in different structural sites, Fe(III) in the tetrahedral site is most reactive and that of cis-octahedral sites the least. These relations are consistent with the layer conductivity and the possible electron transport chain at cell-mineral interface. Biogenic Fe(II) speciates into the four chemical environments in clay minerals: aqueous, structural, complexed to amphoteric surface sites and at exchange sites. The sorbed Fe(II) both to cell and mineral surfaces exerts strong inhibitory effect due to the blockage of electron transfer chain or electrode passivation. Therefore the measured extent of Fe(III) reduction in batch experiments always underestimates the 'bioavailable' Fe(III) in minerals. The interplay of these factors can be modeled by considering the reactive surface site concentration, surface saturation, Fe(II) production and its sorption to mineral and cell surfaces resulting in surface inhibition.