Undiagnosed diabetes poses significant public health challenges in Ghana. Numerous factors may influence the prevalence of undiagnosed diabetes among adults, and therefore, using a model that takes into account the intricate network of these relationships should be considered. Our goal was to evaluate fasting plasma levels, a critical indicator of diabetes, and the associated direct and indirect associated or protective factors. This research employed a cross-sectional survey to sample 1200 adults aged 25-70 years who perceived themselves as healthy and had not been previously diagnosed with diabetes from 13 indigenous communities within the Cape Coast Metropolis, Ghana. Diabetes was diagnosed based on the American Diabetes Association (ADA) criteria for fasting plasma glucose, and lipid profiles were determined using Mindray equipment (August 2022, China). A stepwise WHO questionnaire was used to collect data on sociodemographic and lifestyle variables. We analyzed the associations among the exogenous, mediating, and endogenous variables using a generalized structural equation model (GSEM). Overall, the prevalence of prediabetes and diabetes in the Cape Coast Metropolis was found to be 14.2% and 3.84%, respectively. In the sex domain, females had a higher prevalence of prediabetes (15.33%) and diabetes (5.15%) than males (12.62% and 1.24%, respectively). Rural areas had the highest prevalence, followed by peri-urban areas, whereas urban areas had the lowest prevalence. In the GSEM results, we found that body mass index (BMI), triglycerides (TG), systolic blood pressure (SBP), gamma-glutamyl transferase (GGT), and female sex were direct predictive factors for prediabetes and diabetes, based on fasting plasma glucose (FPG) levels. Indirect factors influencing diabetes and prediabetes through waist circumference (WC) included childhood overweight status, family history, age 35-55 and 56-70, and moderate and high socioeconomic status. High density lipoprotein (HDL) cholesterol, childhood overweight, low physical activity, female sex, moderate and high socioeconomic status, and market trading were also associated with high BMI, indirectly influencing prediabetes and diabetes. Total cholesterol, increased TG levels, WC, age, low physical activity, and rural dwellers were identified as indirectly associated factors with prediabetes and diabetes through SBP. Religion, male sex, and alcohol consumption were identified as predictive factors for GGT, indirectly influencing prediabetes and diabetes. Diabetes in indigenous communities is directly influenced by blood lipid, BMI, SBP, and alcohol levels. Childhood obesity, physical inactivity, sex, socioeconomic status, and family history could indirectly influence diabetes development. These findings offer valuable insights for policymakers and health-sector stakeholders, enabling them to understand the factors associated with diabetes development and implement necessary public health interventions and personalized care strategies for prevention and management in Ghana.