Petroleum contaminants are exposed to weathering when released into environment, resulting in the alteration of their chemical composition. Here, we investigated microbial communities through the soil profile at an industrial site, which was exposed to various petroleum products for over 50 years. The petroleum is present as light non-aqueous phase liquid (LNAPL) and is undergoing natural source zone depletion (NSZD). Microbial community composition was compared to the contaminant type, concentration, and its depth of obtained soil cores. A large population of Archaea, particularly Methanomicrobia and Methanobacteria and indication of complex syntrophic relationships of methanogens, methanotrophs and bacteria were found in the contaminated cores. Different families were enriched across the LNAPL types. Results indicate methanogenic or anoxic conditions in the deeper and highly contaminated sections of the soil cores investigated. The contaminant was highly weathered, likely resulting in the formation of recalcitrant polar compounds. This research provides insight into the microorganisms fundamentally associated with LNAPL, throughout a soil depth profile above and below the water table, undergoing NSZD processes at a legacy petroleum site. It advances the potential for integration of microbial community effects on bioremediation and in response to physicochemical partitioning of LNAPL components from different petroleum types.