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Coronary vascular disease (CVD) is the leading cause of mortality worldwide, while type 2 diabetes mellitus (T2DM) coexists in up to 40% of patients with established CVD and nearly doubles the risk of death. Heart rate recovery (HRR) is a recognized predictor of adverse cardiovascular outcomes, but the specific influence of T2DM on HRR remains incompletely understood. Metabolic inflexibility—reflected by a reduced peak respiratory exchange ratio (RER)—is characteristic of T2DM and may mediate its impact on HRR. We investigated this potential mediation relationship in post-percutaneous coronary intervention (PCI) patients. We performed a single-center, retrospective cross-sectional study of 275 post-PCI patients at Beijing Anzhen Hospital from September 2023 to August 2024. Demographics, traditional cardiovascular risk factors, and physical activity status were recorded. Cardiopulmonary exercise testing (CPET) provided peak RER (RERpeak), ΔRER, and first-minute after peak exercise HRR (HRR1). Using multivariate regression, we assessed associations among T2DM, RER parameters, and HRR1, while adjusting for potential confounders. Mediation analysis evaluated whether RER parameters mediated the relationship between T2DM and HRR1. Subgroup analyses were conducted according to β-blocker use. A total of 275 post-PCI patients were included (198 without T2DM, 77 with T2DM). Compared with non-diabetic participants, those with T2DM exhibited significantly lower RERpeak (1.12 ± 0.07 vs. 1.17 ± 0.08; p < 0.001) and ΔRER (0.27 ± 0.08 vs. 0.31 ± 0.10; p = 0.001). T2DM was independently associated with worse HRR1 (β = − 2.47, 95% CI: − 4.53 to − 0.41, p = 0.0197) after adjustment. Both RERpeak and ΔRER were negatively correlated with T2DM and positively correlated with HRR1. Mediation analysis showed that RERpeak partially mediated 25.06% of T2DM’s adverse effect on HRR1, while ΔRER accounted for 17.62%. Subgroup analyses revealed that in patients not receiving β-blockers, RERpeak mediated 28.46% of the T2DM-HRR1 association, while ΔRER accounted for 13.51%; however, this mediation effect was not evident in β-blocker users. In this post-PCI population, metabolic inflexibility partially mediated the negative association between T2DM and impaired post-exercise HRR. These findings highlight the need to improve metabolic flexibility in diabetic patients as part of risk stratification and targeted therapeutic interventions. What is currently known about this topic? What is the key research question? Does metabolic inflexibility mediate the association between type 2 diabetes and impaired heart rate recovery in post-PCI patients? What is new? How might this study influence clinical practice? Interventions moving beyond glucose control to include metabolic flexibility optimization in comprehensive diabetes-CVD management.