Geographical disparities in abdominal obesity (AO) exist in low-income countries due to major demographic and structural changes in urban and rural areas. We aimed to investigate differences in the urban–rural prevalence of AO in the Malawi population between 2009 and 2017. We conducted a secondary analysis of data from the Malawi 2009 and 2017 STEPS surveys. AO (primary outcome) and very high waist circumference (secondary outcome) were defined using WHO criteria. Prevalence estimates of AO and very high waist circumference (WC) were standardized by age and sex using the age and sex structure of the adult population in Malawi provided by the 2018 census. A modified Poisson regression analysis adjusted for sociodemographic covariates was performed to compare the outcomes between the two groups (urban versus rural). In total, 4708 adults in 2009 and 3054 adults in 2017 aged 25–64 were included in the study. In 2009, the age–sex standardized prevalence of AO was higher in urban than rural areas (40.9% vs 22.0%; adjusted prevalence ratio [aPR], 1.51; 95% confidence interval [CI], 1.36–1.67; p < 0.001). There was no significant trend for closing this gap in 2017 (urban 37.0% and rural 21.4%; aPR, 1.48; 95% CI, 1.23–1.77; p < 0.001). This urban–rural gap remained and was slightly wider when considering the ‘very high WC’ threshold in 2009 (17.0% vs. 7.1%; aPR, 1.98; 95%CI, 1.58–2.47; p < 0.001); and in 2017 (21.4% vs. 8.3%; aPR, 2.03; 95%CI, 1.56–2.62; p < 0.001). Significant urban–rural differences exist in the prevalence of AO and very high WC in Malawi, and the gap has not improved over the last eight years. More effective weight management strategies should be promoted to reduce health care disparities in Malawi, particularly in urban areas.