Although infections are frequent in patients with pulmonary embolism (PE), its effect on adverse outcome risk remains unclear. We investigated the incidence and prognostic impact of infections requiring antibiotic treatment and of inflammatory biomarkers (C-reactive protein [CRP] and procalcitonin [PCT]) on in-hospital adverse outcomes (all-cause mortality or hemodynamic insufficiency) in 749 consecutive PE patients enrolled in a single-centre registry. Adverse outcomes occurred in 65 patients. Clinically relevant infections were observed in 46.3% of patients and there was an increased adverse outcome risk with an odds ratio (OR) of 3.12 (95% confidence interval [CI] 1.70–5.74), comparable to an increase in one risk class of the European Society of Cardiology (ESC) risk stratification algorithm (OR 3.45 [95% CI 2.24–5.30]). CRP > 124 mg/dL and PCT > 0.25 µg/L predicted patient outcome independent of other risk factors and were associated with respective ORs for an adverse outcome of 4.87 (95% CI 2.55–9.33) and 5.91 (95% CI 2.74–12.76). In conclusion, clinically relevant infections requiring antibiotic treatment were observed in almost half of patients with acute PE and carried a similar prognostic effect to an increase in one risk class of the ESC risk stratification algorithm. Furthermore, elevated levels of CRP and PCT seemed to be independent predictors of adverse outcome.