<b><i>Background:</i></b> Electromagnetic navigation bronchoscopy (ENB) is a minimally invasive technology for the diagnosis of peripheral pulmonary nodules. However, ENB is limited by the lack of real-time confirmation of various biopsy devices. Cone-beam computed tomography (CBCT) could increase diagnostic yield by allowing real-time confirmation to overcome the inherent divergence of nodule location. <b><i>Objectives:</i></b> The aim of this study was to assess the diagnostic yield of ENB plus CBCT as compared with ENB alone for biopsy of peripheral lung nodules. <b><i>Method:</i></b> We conducted a retrospective study of patients undergoing ENB before and after the implementation of CBCT. Data from 62 consecutive patients with lung nodules located in the outer two-thirds of the lung who underwent ENB and combined ENB-CBCT were collected. Radial endobronchial ultrasound was used during all procedures as well. Diagnostic yield was defined as the presence of malignancy or benign histological findings that lead to a specific diagnosis. <b><i>Results:</i></b> Thirty-one patients had ENB-CBCT, and 31 patients had only ENB for peripheral lung lesions. The median size of the lesion for the ENB-CBCT group was 16 (interquartile range (IQR) 12.6–25.5) mm as compared to 21.5 (IQR 16–27) mm in the ENB group (<i>p</i> = 0.2). In the univariate analysis, the diagnostic yield of ENB-CBCT was 74.2% and ENB 51.6% (<i>p</i> = 0.05). Following multivariate regression analysis adjusting for the size of the lesion, distance from the pleura, and presence of bronchus sign, the odds ratio for the diagnostic yield was 3.4 (95% CI 1.03–11.26, <i>p</i> = 0.04) in the ENB-CBCT group as compared with ENB alone. The median time for the procedure was shorter in patients in the ENB-CBCT group (74 min) than in those in the ENB group (90 min) (<i>p</i> = 0.02). The rate of adverse events was similar in both groups (6.5%, <i>p</i> = 0.7). <b><i>Conclusions:</i></b> The use of CBCT might increase the diagnostic yield in ENB-guided peripheral lung nodule biopsies. Future randomized clinical trials are needed to confirm such findings.