This study investigated how disturbances in glucose metabolism relate to periodontitis among overweight and obese adults. A total of 870 diabetes-free participants aged 40–65 years completed a three-year follow-up as part of the San Juan Overweight Adults Longitudinal Study. Prediabetes was defined according to ADA criteria using fasting glucose, 2-hour post-load glucose, and HbA1c levels. Periodontal status was determined using NHANES protocols. To explore the association between initial glucose regulation indicators and periodontal outcomes after three years, multivariable linear regression analyses were performed while controlling for potential confounders. The findings revealed no significant link between impaired glucose metabolism and average pocket depth (PD), clinical attachment loss (CAL), or the proportion of sites with PD ≥5 mm. Interestingly, individuals with impaired glucose tolerance (IGT) showed a lower average percentage of sites with CAL ≥5 mm (β = −1.6, p = 0.037). Both prediabetes and impaired fasting glucose (IFG) correlated with a reduction in the mean percentage of sites exhibiting PD ≥5 mm (β = −1.4, p = 0.022; β = −1.6, p = 0.032, respectively). Additionally, IFG and IGT were linked to decreased percentages of sites with CAL ≥5 mm (β = −1.6, p = 0.038; β = −1.9, p = 0.020, respectively). Overall, these results indicate that neither prediabetes nor insulin resistance at baseline consistently predicted periodontitis progression over the three-year observation period.