Background/Objectives: Digital impressions are increasingly used to manage Cleft lip and/or palate (CL/P), potentially offering advantages over traditional methods. This laboratory investigation sought to evaluate the impact of scanning tip sizes, different scanners, and scanning strategies on intraoral scanning in neonates with CL/P. Methods: Ten soft acrylic models were used to simulate the oral anatomy of neonates with CL/P, evaluating parameters such as the ability of different scanning tips to capture alveolar cleft depth, scanning time, number of scan stops, and scan quality. The study utilised various scanning tips, including the Carestream normal tip, Carestream side tip, and Trios 4 scanner tip to assess the alveolar cleft depth measurements. The Trios 4, Carestream, and iTero scanners were evaluated for the time taken, number of scan stops during cleft-unobstructed scanning and cleft-obstructed scanning. The quality of all scanned images was analysed. Results: The findings showed comparable accuracy in capturing alveolar cleft depth with the three-scanning tip (p > 0.05). Scanning time and the number of scan stops did not significantly differ across the three scanners and various scanning strategies employed (p > 0.05). However, scanning with the cleft obstructed required less time and resulted in fewer scan stops compared to cleft -unobstructed scanning. Despite these results, all scanners failed to record the deepest part of the alveolar cleft, highlighting a limitation in current scanning technology for neonates with CL/P. Conclusions: The study recommends enhancing intraoral scanning in this population by adjusting tip size, improving clinician training, optimizing protocols, and conducting further research to improve techniques.