Bronchoscopic diagnosis of small peripheral lung lesions suspected of lung cancer remains a challenge. A successful endobronchial diagnosis comprises navigation, confirmation, and tissue acquisition. In all steps, 3-dimensional information is essential. Cone-beam computed tomography (CBCT) imaging can provide computed tomography information and 3-dimensional augmented fluoroscopy imaging. We assessed whether CBCT imaging can improve navigation and diagnosis of peripheral lesions by 2 clinical workflows with a cross-over design: (1) a primary CBCT and radial endobronchial ultrasound mini probe imaging-based approach and (2) a primary electromagnetic navigation (EMN) and radial endobronchial ultrasound mini probe imaging-based approach. All patients with a peripheral lung lesion biopsy indication were eligible for study inclusion and randomly assigned to study arms. Commercially available equipment was used. The main study goals were to assess CBCT-confirmed navigation success and diagnostic accuracy. Surgery or unambiguous clinical follow-up served as the gold standard. Eighty-seven patients with 107 lesions were included. Lesion mean longest axis size in the CBCT arm was 16.6 mm (n=47) and 14.2 mm in the EMN arm (n=40). The primary CBCT approach and primary EMN approach had 76.3% and 52.2% navigation success, respectively. Addition of EMN to the CBCT approach increased navigation success to 89.9%. Addition of CBCT imaging to the EMN approach significantly increased navigation success to 87.5% per lesion. The overall diagnostic accuracy per patient was significantly lower than the navigation success, being 72.4%. CBCT imaging is a valuable addition to navigation bronchoscopy. Although overall navigation success was high, the diagnostic accuracy remains to be improved. Future research should focus on improving the tissue acquisition methodology.