Clinical decision-making for diagnosing and treating oral and dental diseases consolidates multiple sources of complex information, yet individual clinical judgements are often made intuitively on limited heuristics to simplify decision making, which may lead to errors harmful to patients. This study aimed at systematically evaluating dental practitioners’ clinical decision-making processes during diagnosis and treatment planning under uncertainty. A scoping review was chosen as the optimal study design due to the heterogeneity and complexity of the topic. Key terms and a search strategy were defined, and the articles published in the repository of the National Library of Medicine (MEDLINE/PubMed) were searched, selected, and analysed in accordance with PRISMA-ScR guidelines. Of the 478 studies returned, 64 relevant articles were included in the qualitative synthesis. Studies that were included were based in 27 countries, with the majority from the UK and USA. Articles were dated from 1991 to 2022, with all being observational studies except four, which were experimental studies. Six major recurring themes were identified: clinical factors, clinical experience, patient preferences and perceptions, heuristics and biases, artificial intelligence and informatics, and existing guidelines. These results suggest that inconsistency in treatment recommendations is a real possibility and despite great advancements in dental science, evidence-based practice is but one of a multitude of complex determinants driving clinical decision making in dentistry. In conclusion, clinical decisions, particularly those made individually by a dental practitioner, are potentially prone to sub-optimal treatment and poorer patient outcomes.