The diagenetic mineral assemblages in petroleum reservoirs control the formation fluid pH and pCO2. Anaerobic biodegradation of petroleum is controlled by the transfer of electrons from reduced organic species to inorganic, redox sensitive, aqueous and mineral species in many cases through intermediates such as H2 and CH3COO−. The terminal electron accepting reactions induce the dissolution or precipitation of the same minerals that control the ambient pH and pCO2 in petroleum reservoirs. In this study, we develop a model for anaerobic biodegradation of petroleum that couples the production of acetate and H2 to ‘late stage’ diagenetic reactions. The model reveals that the principal terminal electron accepting process and electron donor control the type of diagenetic reaction, and that the petroleum biodegradation rate is controlled through thermodynamic restriction by the minimum ΔG required to support a specific microbial metabolism, the fluid flux and the mineral assemblage. These relationships are illustrated by modeling coupled microbial diagenesis and biodegradation of the Gullfaks oil reservoir. The results indicate that the complete dissolution of albite by acids generated during oil biodegradation and the corresponding elevated pCO2 seen in the Gullfaks field are best explained by methanogenic respiration coupled to hydrocarbon degradation and that the biodegradation rate is likely controlled by the pCH4. Biodegradation of Gullfaks oil by a consortium that includes either Fe3+-reducing or -reducing bacteria cannot explain the observed diagenetic mineral assemblage or pCO2. For octane, biodegradation, not water washing, was the principal agent for removal at fluid velocities <20 m Myr−1.