This study investigated the behaviour of pathogens and microbial indicators during dewatering of sludge from an upflow anaerobic sludge blanket (UASB) reactor treating real domestic wastewater under tropical conditions. The sludge was dewatered in air-drying beds during wet and dry seasons and was monitored for 90 days. Culture-based methods, direct microscopy identification and quantitative polymerase chain reaction assays, were used to evaluate pathogenic and microbiological indicator microorganisms in the sludge. Thermotolerant coliforms and coliphages (somatic and male F-specific) were monitored as bacterial and viral indicators, respectively. Pathogenic organisms monitored included Salmonella spp., Salmonella Typhimurium, Salmonella Enteritidis, pathogenic Escherichia coli strains (intimin-coding genes), Campylobacter jejuni, Cryptosporidium spp., adenovirus, and viable helminths eggs. Results revealed that microbial indicators did not show a significant variation between the dry and wet seasons, as it was verified for some pathogens. During the 90 days of sludge dewatering, the air-drying bed was able to remove microbial indicators and the pathogenic organisms E. coli, S. Typhimurium, and Cryptosporidium spp. (when present). Pathogenic C. jejuni, S. Enteriditis, and adenovirus decreased 0.5–1.7, 0.3–0.4, and 2.6–4.8 log units, respectively. These results highlight the potential of air-drying beds as a simple and low-cost process for sludge dewatering and hygienisation.