Background: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant morbidity and mortality worldwide since its emergence in 2019. While primarily a respiratory illness, COVID-19 can also affect other organ systems, including the vascular and gastrointestinal systems. COVID-19 infection is linked to both venous and arterial thrombosis, with numerous studies indicating a heightened risk of pulmonary embolism (PE) among patients. Autopsies have revealed pulmonary vasculature thrombosis and bowel ischemia in COVID-19 cases. Aim: This prospective cross-sectional study aimed to assess radiological pulmonary vascular changes, specifically pulmonary embolism (PE), and gastrointestinal changes in COVID-19 patients referred to a tertiary healthcare center in Chennai, India. Methods: CT pulmonary angiography (CTPA) and contrast-enhanced CT of the abdomen were conducted in 100 COVID-19 positive patients meeting the inclusion and exclusion criteria. Evaluation of pulmonary vascular changes and bowel changes was performed by a radiologist with five years of experience. Subsequently, statistical analysis was carried out to determine the significance of the relationship between COVID-19 patients and the occurrence of pulmonary vascular and bowel changes. Results: In our study, 11 patients exhibited pulmonary thromboembolism, and 7 patients showed significant bowel changes. There is a positive correlation between the prevalence of PE in COVID-19 patients. PE was diagnosed at a mean of 11 days from the onset of the disease. Out of 24 patients with severe acute respiratory illness (SARI), 7 showed PE in CTPA. Additionally, out of 10 mechanically ventilated patients, 7 had PE in CTPA. Among the 7 patients with bowel changes, 4 had PE in CTPA, indicating a significant association with PE. The observed bowel changes were attributed to intravascular thrombosis. Conclusion: Based on our findings, individuals with COVID-19 often develop pulmonary emboli and bowel changes. Multivariate analyses revealed a connection between invasive mechanical ventilation and PE. Our results suggest that patients with severe clinical manifestations of COVID-19 may also have concurrent acute PE. Thus, for these patients, utilizing contrast-enhanced CT scans instead of standard non-contrast CT scans may aid in treatment decision-making.