This study investigated the efficiency of the treatment processes of wastewater treatment plants (WWTPs) to remove severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper mild mottle virus (PMMoV) from the wastewater and sewage sludge, as well as the influence of the mode of operation on the quality of the treated wastewater. SARS-CoV-2 and PMMoV were detected and quantified at different stages of the wastewater and sludge treatment process of three major WWTPs in Stockholm, Sweden. The results showed that primary, biological, and advanced membrane treatment processes are effective in removing SARS-CoV-2 from the wastewater with removal efficiencies of 99–100 % for all WWTPs, while the virus was accumulated in the primary and waste-activated sludges due to higher affinity to biosolids. Operation strategies such as bypass reintroduced the virus into the treated wastewater. The WWTPs achieved relatively low PMMoV removal efficiencies (63–87 %) most probably due to the robust capsid structure of the virus. Anaerobic digestion could not completely remove SARS-CoV-2 and PMMoV from the sludge leading to increased levels of SARS-CoV-2 and PMMoV in dewatered sludge. The study gives an overview of WWTPs’ role in tackling pathogen spread in society in the event of a pandemic and disease breakout.