In pedogenic and diagenetic processes, clay minerals transform from pre-existing phases to other clay minerals via intermediate interstratified clays. Temperature, pressure, chemical composition of fluids, and time are traditionally considered to be the important geological variables for clay mineral transformations. Nearly ten years ago, the role of microbes was recognized for the first time, where microbial reduction of structural Fe(III) in smectite resulted in formation of illite under ambient conditions within two weeks. However, the opposite process, the oxidation of structural Fe(II) in illite has not been studied and it remains unclear whether or not this process would result in the back reaction, e.g., from illite to smectite. The overall objective of this study was to investigate biological oxidation of structural Fe(II) in illite coupled with nitrate reduction and the effect of this process on clay mineral transformation. Laboratory incubations were set up, where structural Fe(II) in illite served as electron donor, nitrate as electron acceptor, and Pseudogulbenkiania sp. strain 2002 as mediator. Solution chemistry and gas composition were monitored over time. Mineralogical transformation resulting from bioreduction was characterized with X-ray diffraction and scanning and transmission electron microscopy. Our results demonstrated that strain 2002 was able to couple oxidation of structural Fe(II) in illite with reduction of nitrate to N 2 with nitrite as a transient intermediate. This oxidation reaction resulted in transformation of illite to smectite and ultimately to kaolinite (illite→smectite→kaolinite transformations). This study illustrates the importance of Fe redox process in mediating the smectite-illite mineral cycle with important implications for Fe redox cycling and mineral evolution in surficial earth environments.