Overcoming the TB epidemic requires moving past expanding the coverage of healthcare services and looking to improve the quality of TB services. During COVID-19, the suboptimal state of TB services has further deteriorated, and little is known about how these services have fared after the pandemic. The study aims to assess the quality TB diagnostic services in primary health care (PHC) clinics in the eThekwini district, South Africa. Twenty-one clinics with the lowest and highest headcounts from each region of eThekwini were purposively selected. An audit tool adapted from the United States Agency for International Development (USAID) and the national TB guidelines was used to collect data on six different audit components. To assess quality, a 3-point scale was used where clinics could get a rating of either excellent, moderate, or poor performance. Descriptive statistics were employed to summarize and analyze clinic scores in Stata v15.1. Additionally, associations between clinic scores and clinic characteristics were investigated using Pearson’s pairwise correlation coefficient and a linear regression model, where p < 0.05 was the measure of statistical significance. The audit found that the quality of diagnostic services in eThekwini was moderate. The gaps that required addressing were the lack of TB training among staff, adherence to infection prevention and control practices, and contact screening. Without feasible solutions, these will hinder current TB management strategies and slow progress toward ending the TB epidemic.