Purpose: Secondary organizing pneumonia (OP) and acute fibrinous and organizing pneumonia (AFOP) are frequently observed in cases of COVID-19 pneumonia. Nevertheless, the identification of risk factors related to OP/AFOP and their impact on patient outcomes remain inadequately elucidated. Patients and Methods: This retrospective study aimed to identify risk factors associated with OP/AFOP in patients with COVID-19 pneumonia and to compare clinical outcomes between patients with and without OP/AFOP. The study included hospitalized patients with COVID-19 pneumonia admitted between July 1 and September 30, 2021. Factors associated with OP/AFOP were identified using multivariable regression analysis. Additionally, a multivariable Cox proportional hazard model was used to evaluate the association of OP/AFOP with 90-day mortality. Results: Among the 666 hospitalized patients with COVID-19 pneumonia, 53 (8%) developed OP/AFOP during their admission. When compared to patients younger than 50 years old, those aged 50- 70 and over 70 years old exhibited an increased risk of developing OP/AFOP, with adjusted odds ratios (aOR) of 3.87 (95% CI, 1.24- 12.11; P=0.02) and 5.74 (95% CI, 1.80- 18.27; P=0.003), respectively. Other factors associated with OP/AFOP included a history of diabetes mellitus (aOR 2.37; 95% CI, 1.27- 4.44; P=0.01) and patients with oxygen saturation at admission below 88% (aOR 4.52; 95% CI, 1.22- 16.67; P=0.02). Furthermore, the presence of OP/AFOP was correlated with an increased risk of various complications, such as respiratory failure, acute kidney injury, secondary infections, pneumothorax, pneumomediastinum, and pulmonary embolism. Lastly, patients with OP/AFOP exhibited significantly higher 90-day mortality (adjusted hazard ratio 3.40; 95% CI, 1.68- 6.92; P=0.001) compared to those without OP/AFOP. Conclusion: We identified factors associated with an increased risk of OP/AFOP in patients with COVID-19 pneumonia, which included age >= 50 years, a history of DM, and hypoxemia on admission (SpO2 < 88%). Furthermore, our study revealed that OP/AFOP was significantly linked to higher 90-day mortality.