We aimed to report SARS-CoV-2 seroprevalence after the first wave of the pandemic among healthcare workers, and to explore factors associated with an increased infection rate. We conducted a multicentric cross-sectional survey from 27 June to 31 September 2020. For this survey, we enrolled 3454 voluntary healthcare workers across four participating hospitals, of which 83.4% were female, with a median age of 40.6 years old (31.8–50.3). We serologically screened the employees for SARS-CoV-2, estimated the prevalence of infection, and conducted binomial logistic regression with random effect on participating hospitals to investigate associations. We estimated the prevalence of SARS-CoV-2 infection at 5.0% (95 CI, 4.3%–5.8%). We found the lowest prevalence in health professional management support (4.3%) staff. Infections were more frequent in young professionals below 30 years old (aOR = 1.59, (95 CI, 1.06–2.37)), including paramedical students and residents (aOR = 3.38, (95 CI, 1.62–7.05)). In this group, SARS-CoV-2 prevalence was up 16.9%. The location of work and patient-facing role were not associated with increased infections. Employees reporting contacts with COVID-19 patients without adequate protective equipment had a higher rate of infection (aOR = 1.66, (95 CI, 1.12–2.44)). Aerosol-generating tasks were associated with a ~1.7-fold rate of infection, regardless of the uptake of FFP2. Those exposed to clusters of infected colleagues (aOR = 1.77, (95 CI, 1.24–2.53)) or intra-familial COVID-19 relatives (aOR = 2.09, (95 CI, 1.15–3.80)) also had a higher likelihood of infection. This report highlights that a sustained availability of personal protective equipment limits the SARS-CoV-2 infection rate to what is measured in the general population. It also pinpoints the need for dedicated hygiene training among young professionals, justifies the systematic eviction of infected personnel, and stresses the need for interventions to increase vaccination coverage among any healthcare workers.