Abstract Background Clinical outcomes of esophageal and gastric cancer surgery are used for internal and external benchmarking in clinical auditing. For true hospital comparisons, proper case-mix adjustment is required. This study aimed to develop distinct models that allow for case-mix adjusted quality assessment of esophageal and gastric cancer surgery separately and assessed the impact on between-hospital comparisons. Methods This study included all patients undergoing esophagogastric cancer surgery in the Netherlands between 2017-2022 registered in the Dutch Upper Gastrointestinal Cancer Audit. We developed distinct case-mix adjustment models for ten quality indicators (QIs) using backward selection. Model performance of each individual model was evaluated with area-under-the-receiving-operator-curve (AUC) statistics, representing the impact of case-mix on the QI scores. The impact on between-hospital comparisons was quantified using unadjusted and adjusted O/E ratios. Results A total of 4,354 esophageal cancer and 2,109 gastric cancer patients were included. The most frequently selected case-mix variables in the models for all QIs for esophageal cancer surgery were ASA-score, salvage surgery, peripheral vascular disease/aortic aneurysm, chronic lung disease, and tumor histology, whereas for gastric cancer these were age, preoperative weight loss, tumor location, and clinical M stage. The case-mix adjustment models for esophageal and gastric cancer surgery showed low to moderate performance, with internally validated AUCs of 0.58-0.73 and 0.58-0.74, respectively. Case-mix adjustment had low impact on between-hospital comparisons. For both types of cancer, case-mix adjustment had most pronounced impact on between-hospital comparisons for QIs 30-day/in-hospital mortality and failure-to-rescue. Conclusion This study showed that correct quality assessment requires different case-mix models per quality indicator for clinical outcomes of esophageal and gastric cancer surgery. The case-mix models had low to moderate performance scores, suggesting that case-mix has limited impact in between-hospital comparisons of oesopagogastric cancer surgery.