Metabolic syndrome (MetS) describes a condition associated with multiple diseases concomitantly such as diabetes, hypertension, obesity, and dyslipidemia. It has been linked with higher prevalence of cardiovascular disease, atrial fibrillation, and sudden cardiac death. One of the underlying mechanisms could be altered automaticity, which would reflect modifications of sinus node activity. These phenomena can be evaluated analyzing the components of heart rate variability (HRV). Our aim was to examine the modifications of sinus node variability in an isolated heart model of diet-induced obesity and MetS. Male NZW rabbits were randomly assigned to high-fat (HF, n = 8), control (HF-C, n = 7), high-fat, high-sucrose (HFHS, n = 9), and control (HFHS-C, n = 9) groups, fed with their respective diets during 18/28 weeks. After euthanasia, their hearts were isolated in a Langendorff system. We recorded 10-15 min of spontaneous activity. Short RR time series were analyzed, and standard HRV parameters were determined. One-way ANOVA, Kruskal-Wallis test, and bivariate correlation were used for statistical analysis (p < 0.05). We did find an increase in the complexity and irregularity of intrinsic pacemaker activity as shown by modifications of approximate entropy, sample entropy, minimum multiscale entropy, and complexity index in HFHS animals. Even though no differences were found in standard time and frequency-domain analyses, spectral heterogeneity increased in HFHS group. Animal weight and glucose intolerance were highly correlated with the modifications of intrinsic pacemaker variability. Finally, modifications of intrinsic HRV seemed to be reliant on the number of components of MetS present, given that only HFHS group showed significant changes towards an increased complexity and irregularity of intrinsic pacemaker variability.