Background: Cone beam computed tomography (CBCT) enables intraoperative cross-sectional and three-dimensional imaging of the urinary tract. CBCT in a hybrid operating room can be used for intraoperative detection of residual stones and potential additional stone extraction at the end of percutaneous nephrolithotomy (PCNL). This study describes our initial experience with intraoperative CBCT during PCNL and analyzes its role in potentially improving its outcomes. Methods: We conducted a single-center retrospective cohort study at a tertiary referral hospital between 2018 and 2021. The study aimed to evaluate the outcome of patients who underwent intraoperative noncontrast CBCT scan during PCNL. The CBCT scan was performed when the urologist determined the kidney to be endoscopically stone-free. In case any residual fragments were imaged, an additional effort was made to extract them. Patients were divided into three groups based on treatment outcome: stone-free upon CBCT, not stone-free with additional stone extraction after CBCT, and not stone-free without additional stone extraction. Procedure and patient characteristics were recorded to identify factors associated with additional stone extraction during CBCT-assisted PCNL. Results: A total of 102 procedures were included in this study. Intraoperative CBCT scans showed residual calcifications in 58 (57%) cases. In 39 cases, which is 38% of the total population and 61% of the cases with residual calcifications, one or more residual fragments imaged on the intraoperative CBCT-scan were extracted additionally within the same procedure. A higher Guy's Stone Score was associated with a higher likelihood of additionally extracting stones as a result of the CBCT. Conclusions: CBCT-assisted PCNL in a hybrid operating room can lead to additional stone extraction in the same procedure in 37% of all cases and in over 60% of the cases in which residual fragments are imaged. The value of CBCT-assisted PCNL appears to increase in the case of more complex stone surgery cases.