The aim of this study was to comprehensively evaluate the adherence to an externally validated diagnostic pulmonary embolism (PE) protocol. In addition, the long-term prognostic value of biomarkers such as N-terminal pro-B-type natriuretic peptide (NT-proBNP), C-reactive protein (CRP), D-dimer and cardiac troponin T (cTnT) were assessed in patients undergoing computed tomography pulmonary angiography (CTPA) for a suspected PE. Furthermore, this study analyzed the predictive performance of CTPA-derived markers of right ventricular (RV) dysfunction, including contrast agent (CA) reflux, for determining early mortality risk. In total 1001 patients suspected of PE underwent CTPA in the emergency department (ED) in this retrospective study, of whom 22.2% of patients had PE. Firstly, this study found that CTPA was frequently performed even in patients with low to intermediate pre-test probability without D-dimer testing. Secondly, biomarker profiles demonstrated prognostic significance: in confirmed PE, elevated NT-proBNP (>1000ng/L) and CRP (>50mg/L) predicted poor long-term survival, whereas in patients without PE, increases in multiple biomarkers (NT-proBNP, CRP, D-dimer, cTnT) were associated with worse outcomes. Finally, CA reflux into inferior vena cava (IVC) observed in CTPA and elevated NT-proBNP levels emerged as a potential early markers of poor prognosis in PE. These results emphasize the need for consistent use of validated risk scores and D-dimer testing to reduce unnecessary imaging. Furthermore, RV dysfunction markers in CTPA and biomarker assessment could help identifying patients at higher risk for adverse outcomes.