Purpose <p>Heart rate recovery (HRR) indicates post-exercise autonomic regulation and serves as a marker of cardiorespiratory fitness and mortality risk. Autonomic and metabolic recovery are both integral to post-exercise homeostasis, yet how HRR relates to metabolic recovery remains unclear.</p> Methods <p>To address this gap, we analyzed data from a randomized crossover trial in 17 healthy, physically active young men, each performing 30&#xa0;min of both moderate- and vigorous-intensity ergometer cycling. Plasma samples collected before exercise and at multiple recovery time points were analyzed using UPLC–MS/MS–based untargeted metabolomics, covering more than 1000 metabolites. HRR was calculated using a monoexponential decay model, and associations were examined using linear mixed models.</p> Results <p>Individuals with faster HRR exhibited significantly lower post-exercise levels across a range of lipid metabolites, particularly acylcarnitines. These associations were stronger for HRR than VO₂peak and were statistically significant only in the later recovery period (90–180&#xa0;min post-exercise), exclusively following vigorous-intensity exercise. Our findings suggest that HRR reflects post-exercise lipid metabolism under conditions of high metabolic demand. The observed metabolite patterns are indicative of differences in β-oxidation, lipid accumulation, reliance on ω-oxidation, and mitochondrial turnover, and are consistent with more efficient post-exercise lipid metabolism.</p> Conclusion <p>HRR may provide a simple marker of metabolic or cardiorespiratory fitness and could be relevant for monitoring exercise responses and assessing cardiometabolic health. However, confirmation in larger and more diverse cohorts is required.</p> Clinical trials register <p>The trial was registered on October 5, 2017, at the German Clinical Trials Register under the registration number DRKS00009743 (Universal Trial Number of WHO: U1111-1200–2530).</p> Graphical abstract <p></p>