One of the most commonly observed complications after COVID-19 is persistent pulmonary impairment. The aim of this study was to evaluate the impact of individual factors during the acute phase of COVID-19 on subsequent pulmonary function test results. The study involved 46 patients who were admitted to hospital due to respiratory failure caused by SARS-CoV-2 and who were assessed during follow-up visits at 3 and 9 months after discharge. Patients were divided into two subgroups according to the severity of respiratory failure. The severe group included patients requiring mechanical ventilation or HFNOT. The results of the study showed that a severe course of the disease was associated with a lower FVC and a higher FEV1/FVC ratio 3 months after discharge (both p < 0.05). In addition, it has been revealed that the length of hospitalization is a factor that negatively impacts the FEV1, FVC and TLC values measured at follow-up after 3 months. Furthermore, the obtained results identify the presence of cough in the acute phase of the disease as a factor having a positive impact on several PFT parameters (especially the FEV1/FVC ratio) as well as the 6MWT outcome after 3 months. The FVC improved significantly (p < 0.05) between the follow-up visits. The findings may indicate that COVID-19-induced respiratory dysfunction is usually temporary and spontaneously resolves during recovery. Recovery is slower in those who required more intensive oxygenation. The results of this study may be useful in identifying patients who require more intensive and longer rehabilitation after COVID-19.