Biogas is upgraded using an absorption with water-wash technique by 11 of a total of 14 upgrading plants in Sweden. However, problems with microbial growth on the pall rings in the absorption column, and in one case in the desorption column, have a negative impact on the upgrading of raw gas to vehicle gas. Five of the nine biogas plants studied here have experienced problems with microbial growth. The objectives of this study were to identify such microbial growth and to determine possible factors for its control, in order to provide recommendations for process management. A questionnaire was sent out and visits were made to the upgrading plants to collect information about the upgrading process. Phospholipid fatty acid (PLFA) analysis was performed to determine microbial biomass and community structure in samples from four upgrading plants. In samples from two of the plants, methane-oxidizing bacteria (type I methanotrophs) were indicated, while samples from one of the other plants showed biomarkers indicating actinomycetes. Factors affecting development of microbial growth were found to be water quality and the pH and temperature of the process water. Plants that used wastewater in the upgrading process experienced far more problems than those using clean water of drinking quality.