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<i>Background and Objectives:</i> Kidney transplant recipients (KTRs) are at a higher risk of severe COVID-19 development. The course of the infection may vary. Long-term consequences for graft function are still being studied. We investigate whether the clinical course of SARS-CoV-2 infection among KTRs had a long-term effect on graft function. <i>Patients and method:</i> 128 KTRs with confirmed SARS-CoV-2 infection were included in the study. They were divided into two groups: mild (without the need for oxygen therapy; <i>n</i> = 91) and severe (with the need for oxygen therapy; <i>n</i> = 21). Baseline characteristics and medical data, especially creatinine level, estimated glomerular filtration rate (eGFR) CKD-EPI, and proteinuria, were analyzed. The main outcomes were the absolute and relative change in eGFR during the one-year follow-up after COVID-19. In the final models, sex, age, smoking, presence of diabetes mellitus (DM), and cardiovascular disease (CVD) were included. <i>Results:</i> KTRs with severe COVID-19 were older, more likely to smoke, and had DM and CVD more frequently. Our analysis reveals that COVID-19 severity was associated with a significantly more pronounced relative eGFR decline one year after recovery only in males [−13.94 (95% CI: −25.13 to −2.76, <i>p</i> = 0.015) percentage points]. One year after the disease onset, males with a severe course of the infection had a higher eGFR decline than those with a mild one. The COVID-19 severity did not affect eGFR loss in females. <i>Conclusions:</i> In KTRs suffering from COVID-19, deterioration of graft function was noticed. The eGFR decline was associated with disease severity and sex. It indicates a need for further research, observation, and preventive actions for KTRs, especially males.