Background: Patients with severe COVID-19 experience various respiratory complications, which can have potential long-term effects. Objectives: This study investigates the long-term pulmonary consequences of severe COVID-19 and their relationship with the severity of lung involvement. Methods: All patients who survived severe COVID-19 in the ICU were selected for the study. A radiologist reviewed the chest CT scans, and patients were categorized based on their total severity score (TSS) into two groups: Group A (TSS ≤ 7) and Group B (TSS > 7). Patients were followed up after three months with a chest CT scan, spirometry, SpO2 measurement, and a dyspnea score assessment. Results: The mean age was 54.69 ± 12.51 for Group A and 55.31 ± 12.73 for Group B. Groups A and B had 23 (46.9%) and 39 (39.4%) female patients, respectively. Patients in Group B had significantly lower SpO2 and a prolonged length of hospitalization. Group B also experienced more severe dyspnea and reduced lung function, as observed in spirometry during the three-month follow-up. The total severity score decreased significantly after three months in all patients (from 14.42 ± 5.90 to 6.68 ± 4.79; P < 0.001). After logistic regression analysis, non-invasive ventilation was independently associated with a higher TSS (OR = 0.45 when comparing Group A to Group B; P = 0.028). Conclusions: The lungs are the most affected organ by COVID-19, making it crucial to investigate the effects of the virus on pulmonary function. Our study showed that patients with higher TSS experienced greater reductions in lung function during the three-month follow-up. Additionally, the use of non-invasive ventilation was independently associated with a higher TSS in severe COVID-19 cases.