Faecal-oral transmission of SARS-CoV-2 is a hot topic and additional research is needed to elucidate the risks of the novel coronavirus in sanitation systems. This is the first article that investigates the potential health risks of SARS-CoV-2 in sewage to wastewater treatment plants (WWTPs) workers. A quantitative microbial risk assessment (QMRA) is applied for three COVID-19 scenarios (moderate, aggressive and extreme) to study the effect of different stages of the pandemic, in terms of percentage of infected population, on the probability of infection. Results reveal that estimates of viral loads in sewage at the entrance of WWTPs ranged from 1.03×102 to 1.31×104 GC.mL-1 (0.1 to 13.06 PFU.mL-1, respectively) and that estimated risks for the aggressive and extreme scenarios (6.5×10-3 and 3.1×10-2, respectively) were likely to be above a WHO benchmark of tolerable risk used for virus infection of 10-3 and higher than the risk of infection of E. coli, used herein as common pathogen indicator for a relative comparison, thus reinforcing the concern of sewage systems as a transmission pathway of SARS-CoV-2. These findings are helpful as an early-warning tool and in prioritizing upcoming risk management strategies in the sanitation sector during COVID-19 pandemic.