While ground-glass opacity, consolidation, and fibrosis in the lungs are some of the hallmarks of acute SAR-CoV-2 infection, it remains unclear whether these pulmonary radiological findings would resolve after acute symptoms have subsided. We conducted a systematic review and meta-analysis to evaluate chest computed tomography (CT) abnormalities stratified by COVID-19 disease severity and multiple timepoints post-infection. PubMed/MEDLINE was searched for relevant articles until 23 May 2023. Studies with COVID-19-recovered patients and follow-up chest CT at least 12 months post-infection were included. CT findings were evaluated at short-term (1–6 months) and long-term (12–24 months) follow-ups and by disease severity (severe and non-severe). A generalized linear mixed-effects model with random effects was used to estimate event rates for CT findings. A total of 2517 studies were identified, of which 43 met the inclusion (N = 8858 patients). Fibrotic-like changes had the highest event rate at short-term (0.44 [0.3–0.59]) and long-term (0.38 [0.23–0.56]) follow-ups. A meta-regression showed that over time the event rates decreased for any abnormality (β = −0.137, p = 0.002), ground-glass opacities (β = −0.169, p < 0.001), increased for honeycombing (β = 0.075, p = 0.03), and did not change for fibrotic-like changes, bronchiectasis, reticulation, and interlobular septal thickening (p > 0.05 for all). The severe subgroup had significantly higher rates of any abnormalities (p < 0.001), bronchiectasis (p = 0.02), fibrotic-like changes (p = 0.03), and reticulation (p < 0.001) at long-term follow-ups when compared to the non-severe subgroup. In conclusion, significant CT abnormalities remained up to 2 years post-COVID-19, especially in patients with severe disease. Long-lasting pulmonary abnormalities post-SARS-CoV-2 infection signal a future public health concern, necessitating extended monitoring, rehabilitation, survivor support, vaccination, and ongoing research for targeted therapies.