We systematically analyzed and attempted to discuss the possibility that deficiencies of zinc or selenium were associated with the incidence and severity of COVID-19. We searched for published and unpublished articles in PubMed, Embase, Web of Science and Cochrane up to 9 February 2023. And we selected healthy individuals, mild/severe, and even deceased COVID-19 patients to analyze their serum data. Data related to 2319 patients from 20 studies were analyzed. In the mild/severe group, zinc deficiency was associated with the degree of severe disease (SMD = 0.50, 95% CI 0.32–0.68, I 2 = 50.5%) and we got an Egger’s test of p = 0.784; but selenium deficiency was not associated with the degree of severe disease (SMD = − 0.03, 95% CI − 0.98–0.93, I 2 = 96.7%). In the surviving/death group, zinc deficiency was not associated with mortality of COVID-19 (SMD = 1.66, 95%CI − 1.42–4.47), nor was selenium (SMD = − 0.16, 95%CI − 1.33–1.01). In the risk group, zinc deficiency was positively associated with the prevalence of COVID-19 (SMD = 1.21, 95% CI 0.96–1.46, I 2 = 54.3%) and selenium deficiency was also positively associated with the prevalence of it (SMD = 1.16, 95% CI 0.71–1.61, I 2 = 58.3%). Currently, serum zinc and selenium deficiencies increase the incidence of COVID-19 and zinc deficiency exacerbates the disease; however, neither zinc nor selenium was associated with mortality in patients with COVID-19. Nevertheless, our conclusions may change when new clinical studies are published. Supplementary Information The online version contains supplementary material available at 10.1007/s10534-023-00501-0.