Predicting factors of diagnostic yield in electromagnetic navigation bronchoscopy (ENB) have been explored in a number of previous studies based on data from experienced operators. However, little is known about predicting factors when the procedure is carried out by operators in the beginning of their learning curve. We here aim to identify the role of operators’ experience as well as lesion– and procedure characteristics on diagnostic yield of ENB procedures in the hands of novice ENB operators. Four operators from three centers without prior ENB experience were enrolled. The outcome of consecutive ENB procedures was assessed and classified as either diagnostic or non-diagnostic and predicting factors of diagnostic yield were assessed. A total of 215 procedures were assessed. A total of 122 (57%) of the ENB procedures resulted in diagnostic biopsies. Diagnostic ENB procedures were associated with a minor yet significant difference in tumor size compared to non-diagnostic/inconclusive ENB procedures (28 mm vs. 24 mm; p = 0.03). Diagnostic ENB procedures were associated with visible lesions at either fluoroscopy (p = 0.003) or radial endobronchial ultrasound (rEBUS), (p = 0.001). In the logistic regression model, lesion visibility on fluoroscopy, but none of operator experience, the presence of a bronchus sign, lesion size, or location nor visibility on rEBUS significantly impacted the diagnostic yield. In novice ENB operators, lesion visibility on fluoroscopy was the only factor found to increase the chance of obtaining a diagnostic sample.