Background Dialysis confers the highest risk of COVID-19 death among comorbidities predisposing to severe COVID-19. However, reports of COVID-19-associated mortality frequently refer to mortality during the initial hospitalization or first month after diagnosis. Methods In a prospective, observational study, we have analyzed the long-term (one year follow-up) serological and clinical outcomes of 56 hemodialysis patients that were infected by SARS-CoV-2 during the first pandemic wave. COVID-19 was diagnosed by a positive PCR test (n = 37) or by the development of anti-SARS-CoV-2 antibodies (n = 19). Results After over one year of follow-up, 35.7% of hemodialysis patients infected by SARS-COV-2 during the first pandemic wave had died, 6 (11%) during the initial admission, and 14 (25%) died in the following months, mainly within the first 3 months after diagnosis. Overall, 30% of patients died from vascular causes, and 40% from respiratory causes. In adjusted analysis, positive SARS-CoV-2 PCR test for diagnosis (HR 5.18 [1.30–20.65] p = 0.020), higher baseline C reactive protein levels (HR 1.10 [1.03–1.16] p = 0.002) and lower hemoglobin levels (HR 0.62 [0.45–0.86] p = 0.005) were associated with higher one-year mortality. Mortality in the 144 patients that did not have COVID-19 was 21 (14.6%) over 12 months [hazard ratio for death for COVID-19 patients 3.00 (1.62–5.53), log-rank p = 0.00023]. Over the first year, the percentage of patients having anti-SARS-CoV-2 IgG decreased from 36/49 (73.4%) initially to 27/44 (61.3%) at 6 months, and 14/36 (38.8%) at 12 months. Conclusions The high mortality of hemodialysis patients with COVID-19 is not limited to the initial hospitalization. Defining COVID-19 deaths as those occurring within 3 months of a COVID-19 diagnosis may better represent the burden of COVID-19. In hemodialysis patients, the anti-SARS-CoV-2 IgG response was suboptimal and short-lived.