Microbial processes are fundamental in nutrient cycling and remineralization in marine sediments. To understand how ocean acidification (OA) may influence sediment microbial diversity and activity, naturally CO2-rich sites are increasingly being used. However, the characterization of naturally CO2-rich sites is often limited to OA-related variables, neglecting additional variables that may obscure OA effects, especially when the CO2 increase is caused by geological processes. Here, we reevaluated the factors affecting changes in microbial communities at volcanic CO2 seeps in Papua New Guinea based on a comprehensive characterization of the conditions in the sediment. Microbial community composition was assessed using molecular fingerprinting and amplicon sequencing. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. In-situ microprofiles and trace element concentrations further showed a variation in the strength of the hydrothermal signature of the sediment at similar pH allowing the identification of sites which may better represent future OA than others. At these sites, changes in the microbial community may have implications for element cycling in the sediment. We recommend focusing on a detailed environmental characterization in future OA research, to ensure better comparability between studies and a more reliable selection of naturally CO2-rich sites.