Background: Stunting is highly prevalent in children under 5 years of age, especially in low and middle-income countries, with majority achieving catch-up growth (CUG) in subsequent years. CUG can be associated with development of obesity and abnormal biochemical profiles, which is being investigated in this current study in a birth cohort in Southern India. Methods: An Indian birth-cohort recruited between 2010 and 2012 from urban slums in Vellore, India, was followed up at both 9 and 12 years of age. Along with anthropometric and cognitive measurements, blood analyses evaluated fasting lipid and glucose profiles. Children were divided into groups based on stunting at each time point as well as catch-up growth, and a regression model was utilised to evaluate their association with metabolic profiles. Results: At 2 years, 94/203 (46.31%) children were stunted, out of whom 39.36% caught up in stature at 5 years and 38.3% at 9 years of age. Height, weight, body mass index (BMI), and waist circumference increased significantly between 9 and 12 years of age. Among 9-year-olds, 82.6% had at least one lipid abnormality , which increased to 90.1% by 12-years, specifically in triglycerides and HDLc. CUG did not affect lipid or sugar profile. Linear mixed models showed that concurrent body weight, BMI and waist circumference were associated with high triglycerides and low HDLc. Conclusion: Concurrent weight, BMI and waist circumference influencing these changes highlight probable abdominal fat predominance guiding these patterns rather than CUG. Further studies can explore these patterns in malnourished children with CUG.