Research into the quality of cancer screening programs often lacks the perspective of clinicians, missing insights into the performance of individual hospitals. This retrospective cohort study aimed to identify guideline deviation (specifically, overtreatment and undertreatment) related to the cervical cancer screening program in Dutch hospitals by deterministically linking nationwide insurance data with pathology data for cervical intraepithelial neoplasia (CIN). We then constructed quality indicators using the Dutch CIN guideline and National Health Care Institute recommendations to assess compliance with CIN management, treatment outcomes, and follow-up, using an empirical Bayes shrinkage model to correct for case-mix variation and hospitals with few observations. Data were linked for 115,899 of 125,751 (92%) eligible women. Overtreatment was observed in the see-and-treat approach (immediate treatment) for women with low-grade referral cytology (4%; hospital range, 0%–25%), CIN ≤ 1 treatment specimens (26%; hospital range, 10%–55%), and follow-up cervix cytology ≥2 months before the guideline recommendation after treatment for CIN 2 (2%; hospital range, 0%–9%) or CIN 3 (5%; hospital range, 0%–19%). By contrast, undertreatment was observed for treatment within 3 months after a CIN 3 biopsy result (90%; hospital range 59%–100%) and follow-up ≥2 months beyond the guideline recommendation after treatments for CIN 2 (21%, hospital range 7%–48%) and CIN 3 (20%, hospital range 7%–90%). In conclusion, we found evidence of CIN overtreatment and undertreatment in all measured domains at the hospital level. Guideline adherence could be improved by implementing the developed indicators in an audit and feedback instrument for use by healthcare professionals in routine practice.