Introduction Digestive diseases (DD), such as cirrhosis, upper digestive diseases, inflammatory bowel disease, and pancreatitis, present a significant public health challenge in Sub-Saharan Africa (SSA). The prevalence and impact of these conditions vary widely, highlighting the challenges in managing DD within diverse health systems and sociocultural contexts. Despite their severe impact on morbidity and mortality, they have not garnered as much attention as diseases like HIV/AIDS or malaria. This study utilizes the Global Burden of Disease (GBD) dataset to provide a comprehensive epidemiological overview of DD in SSA, aiming to address gaps in current research and inform effective health policies and interventions.Methods Our study utilized data from the GBD dataset spanning 1990 to 2019, which offers extensive data on mortality, incidence, and disability-adjusted life years (DALYs) across 204 countries. We analyzed trends in the prevalence, deaths, and DALYs of DD, calculating percentage changes and estimated annual percentage changes (EAPCs) in age-standardized rates. Linear regression was employed to compute EAPCs, while Pearson correlation analyses were used to assess the relationships between EAPCs and socio-demographic indices.Results Our study documented a marked increase in total cases of digestive diseases from 1990 to 2019, with prevalence rising by 95.7% for males and 103.5% for females. However, age-standardized prevalence rates per 100,000 individuals declined by 6.9% for males and 7.2% for females. Age-standardized DALY rates for all digestive diseases decreased by 23.7%, and age-standardized death rates reduced by 20.6% for males and 22.1% for females. Specific conditions, such as cirrhosis, experienced significant declines in both DALY and death rates, with reductions of 25.9% and 30.7% for DALYs and 25.6% and 27.6% for death rates in males and females, respectively. The analysis revealed a significant correlation between the EAPCs of DALYs and the Universal Health Coverage (UHC) effective coverage index, with Pearson's r of -0.38 (p-value: 0.008).Conclusion Our study identified significant shifts in the prevalence of digestive diseases in Sub-Saharan Africa, with declines in conditions like cirrhosis and rises in inflammatory bowel disease, influenced by risk factors such as high BMI and drug use. These insights underscore the urgent need for tailored health policies and interventions that address both decreasing and newly emerging health challenges, enhancing public health strategies and ultimately improving health outcomes in the region.