Pulmonary embolism remains a common and potentially deadly disease, despite advances in diagnostic imaging, treatment and prevention. Managing pulmonary embolism requires a multifactorial approach involving risk stratification, determining appropriate diagnostics and selecting individualised therapy. The first part of this article reviewed the pathophysiology, risk factors, clinical presentation, diagnostic evaluation and therapeutic management and early outpatient management of pulmonary embolism. This second part summarises pulmonary embolism in the setting of pregnancy, COVID-19, recurrent disease and chronic thromboembolic pulmonary hypertension.