Hepatitis E virus (HEV) is the main cause of enterically transmitted hepatitis in humans worldwide. Among HEV, genotypes 3 and 4 are considered zoonotic agents associated with domestic pigs and wild boars, showing an increasing trend in Europe. The aim of this study is to contribute data on the prevalence of HEV in wild boars in Southwest Germany and to present a time and cost-effective two-step laboratory diagnostic approach for serological monitoring of blood samples. This method uses enzyme-linked immunosorbent assay (ELISA), followed by testing for HEV RNA by reverse transcription real-time PCR (RT-qPCR). A total of 2295 blood samples were collected in 234 municipalities in 12 counties in the period from 2016 to 2020. There was an overall seroprevalence of 10.8%, ranging from 3.6% to 17.5% per county and 7.5% to 14% per year. Retesting of these blood samples for HEV RNA revealed 15.7% viremic wild boars originating from 30 municipalities in 11 counties. Viremic wild boars were found in seven regional clusters, including 84% of the animals that tested positive for HEV. Seropositive animals <1 year of age were significantly more likely to be viremic than those >1 year. Further characterization of HEV RNA resulted in the identification of genotype 3. Altogether, serological monitoring of the blood samples, complemented by successive and targeted investigations into the presence of HEV RNA based on blood samples, provide reliable information on the seroprevalence and virus load in wild boars, which proved to be a relevant and persistent sylvatic reservoir for HEV.