Malnutrition includes both under-nutrition and over-nutrition, which have negative health impacts and social consequences. The present study aims to understand the demographic dynamics, burden of chronic illnesses, and risk factors associated with malnutrition (stunting, thinness, and obesity) among different age groups in urban and rural areas. Data were collected through a cross-sectional study conducted in an urban area in Hyderabad and four rural villages in Andhra Pradesh. A multivariable mixed-effect logistic regression was used to assess the risk factors associated with malnutrition among different age groups. The final analysis included the data of 10,350 individuals, consisting of 8317 (80.4%) from urban areas and 2033 (19.6%) from rural areas. The number of known cases of hypertension in the urban area was 926 (11.1%) and 114 (5.6%) in the rural areas, and that of diabetes was 511 (6.1%) in the urban area and 104 (5.1%) in the rural areas. The burden of stunting among under-five children and obesity among adults was 33.7% (95% CI; 29.7–37.9) and 47.4% (95% CI; 45.8–49.1), respectively. Adults aged 40–59 years (AOR 1.91; 1.59–2.28) and belonging to a clerical/skilled (AOR 1.32; 1.03–1.71) occupation were at higher odds of obesity compared to their counterparts. Policymakers and health practitioners should consider the insights from our findings to tailor effective interventions to address malnutrition.