<b><i>Introduction:</i></b> Internal audit is one of the tools to ensure safety in patient care. Literature on the internal audit effectiveness (IAE) in patient safety is scarce in Saudi Arabia. This study therefore aimed to assess the factors which influence the IAE in patient safety. <b><i>Methods:</i></b> A cross-sectional study was conducted among primary healthcare centers’ general directors and medical directors in Taif, Saudi Arabia. Data were collected using a validated structured questionnaire in Arabic and English. The questionnaire besides sociodemographics characteristics collected data on support of management, interdepartmental coordination, independence, objectivity, competence, and IAE. Analysis was done on SPSS version 26.0. Pearson correlation was used to see the relationship between factors and the IAE in patient safety. <b><i>Results:</i></b> A total of 94 participants were included in the analysis. The mean scores in each of the domains on a scale of 5 were; support of management 4.04, interdepartmental coordination 3.95, independence 4.03, objectivity 4.20, and competence 4.46, while for the IAE the mean score was 4.36. Correlation analyses found that the IAE was significantly associated with all five factors. All the factors had moderate association except for objectivity which had a weak correlation with IAE. <b><i>Conclusions:</i></b> Overall, there were satisfactory scores for the factors which affect IAE with room for further improvement. All the factors studied were positively associated with the IAE, indicating a need for healthcare organizations to consider these factors while planning internal audit activities. Further research on large scale is required to provide robust and generalizable results.