Abstract Background Suboptimal feeding practices have a negative impact on children’s health and growth in the first 2 years of life and increase their risk of undernutrition, morbidity, and mortality. The aim of the study was to assess the factors that influence infant and young child feeding practices among urban mothers in a hospital setting at Karachi, Pakistan. Methods A longitudinal multi-center cohort study was conducted in four countries, MULTICENTER BODY COMPOSITION REFERENCE STUDY (MBCRS) to produce normal body composition reference data in healthy infants from 3 months to 24 months of age. Repeated anthropometric (weight, length and head circumference) and body composition measurements using “deuterium dilution method” along with 24-h dietary recall questionnaires were performed on 250 healthy term infants at 3, 6, 9, 12, 18, and 24 months of age. The 24-h dietary recall data from this study was used to assess the breastfeeding and complementary feeding practices in children aged 6–24 months. Results A total of 250 healthy infants were enrolled in the study. A majority of newborns (75.4%) were exclusively breastfed till 3 months of age; however, by 6 months of age, only 30.2% of infants were exclusively breastfed. Only 44.1% of children aged 6–24 months achieved minimum dietary diversity (MDD), 84.7% achieved minimum meal frequency (MMF), and 44.1% achieved a minimum acceptable diet (MAD). 71.4% achieved MDD and MAD and 100% achieved MMF at 24 months. The bivariate analysis found that breastfed children (OR 3.93, 95% CI 2.72–5.68), with employed mothers (OR 1.55, 95% CI 1.06–2.27) who had graduated from secondary school (OR 1.45, 95% CI 1.08–1.94) were more likely to meet minimum dietary diversity. The multivariable analysis showed that only the child’s age was significantly associated with MDD (p value< 0.0001), with the likelihood of meeting MDD increasing as the children aged; 9 months (OR 18.96, 95% CI 6.63–54.19), 12 months (OR 40.25, 95% CI 14.14–114.58), 18 months (OR 90.02, 95% CI 30.84–262.77) and 24 months (OR 82.14, 95% CI 27.23–247.83). Conclusion Our study revealed that Infant and young child feeding practices are significantly associated with maternal education, employment, and the child’s age. Therefore, it is essential that investments be made towards protective breastfeeding and complementary feeding policies and legislations, emphasis on female education and ensuring the availability of affordable nutritious and diverse foods.