In recent years, most South African (SA) municipalities still need to produce clean audits. In 2018 and 2019, most municipalities in SA needed better-quality financial statements and performance reports. Misrepresentation of financial statements in audit reports is linked to inadequate governance, misappropriation of public funds and poor public service delivery. It is upon this background that this study aimed to: (i) assess perceptions of municipality middle management employees on factors affecting auditing, (ii) evaluate the differences in perceptions among municipality middle management employees on factors affecting auditing, (iii) measure the effect of factors affecting auditing on overall clean audit and (iv) establish the effect of clean audit on service delivery at two municipalities in Mpumalanga province. Using a structured questionnaire, a quantitative descriptive approach methodology was employed to collect data from a minimum sample of 294 employees in the middle management category working within the accounting and finance department at two municipalities in Mpumalanga province, SA. SPSS v28 was used to conduct descriptive and multivariate analyses, including mean, analysis of variance (ANOVA), correlation, and regression analysis. Results indicated that employees from the clean audit municipality had positive perceptions of factors affecting clean audit, while employees from the municipality with an unclean audit had negative perceptions. It was also concluded that factors affecting auditing had a statistically significant positive effect on clean audits. The findings in this study led to significant implications for theory and practice.