(1) Background: Prediabetes represents reversible glycemic abnormalities between normal glucose regulation and diabetes. Indonesia has a high burden of non-communicable diseases, such as diabetes. This study aims to evaluate the impact of lifestyle changes on prediabetes and diabetes in rural and urban populations. (2) Methods: This is a repeated cross-sectional study, and data were obtained from Basic Health Research (RISKESDAS) in 2013 and 2018. (3) Results: The study found that urban populations who ate >3 days/week of vegetables had a lower proportion of prediabetes and diabetes. Rural populations with 2 days/week of vegetable consumption had a higher risk of prediabetes in 2018. From 2013 to 2018, urban and rural populations consumed excessive amounts of sweet food/drink, salty food, fatty/cholesterol/fried food, and meat/chicken/fish-based food with preservatives. In 2018, urban and rural populations who consumed sweet food/drink more than once daily had a higher risk of prediabetes and diabetes. The prevalence of active physical activity declined in normoglycemic individuals, while it increased in prediabetes and diabetes in urban and rural areas. In 2013, physical activity was a protective factor for prediabetes. (4) Conclusions: Lifestyle changes impacted prediabetes and diabetes prevalence. Further research is needed to promote healthy diets and lifestyle modifications.