SARS-CoV-2, the virus behind the COVID-19 pandemic, affects multiple organs, including the male reproductive system. The male reproductive tract expresses ACE-2, the primary viral entry receptor, in spermatogonia, Leydig, and Sertoli cells. While viral infections can harm male fertility through cytokine storms, the effects of SARS-CoV-2 on fertility are still unclear. Thus, this study aimed to examine the impact of COVID-19 on the male reproductive tract. Semen samples from 20 patients, collected 3 months post-SARS-CoV-2 infection, revealed the presence of ACE2 and TMPRSS2 receptors in both plasmatic and spermatozoa fractions. Five patients showed viral RNA-dependent RNA polymerase (RdRp), indicating potential viral persistence. Elevated levels of inflammatory cytokines and chemokines were observed in the plasmatic fraction, suggesting a persistent inflammatory condition affecting sperm vitality. Immune cell populations associated with viral clearance were identified in the semen fraction, correlating with receptor expression and inflammatory cytokines. To address SARS-CoV-2 uncertainties in reproductive medicine, we assessed the virus’s presence in seminal fluid before and after cryopreservation using slow freezing and vitrification. Our study confirms the safety of both techniques in preserving male fertility for assisted reproductive technology programs. In conclusion, our study highlights the impact of SARS-CoV-2 on male reproductive health, emphasizing the persistence of viral entry receptors, potential viral RNA presence, the inflammatory environment, and the involvement of immune populations in the male reproductive tract post-infection. Importantly, we confirm the safety of conventional freezing and vitrification techniques for preserving male fertility in assisted reproductive technology programs amidst the COVID-19 pandemic.