Optimal infant nutrition is crucial for good health and survival. HIV-exposed infants have a greater incidence of low birthweight than HIV-unexposed infants, predisposing them to malnutrition and a greater risk of HIV infection. A 12-month longitudinal study was conducted on 166 HIV-exposed infants, assessing nutritional status at 6 weeks, 6 months, and 12 months. Fisher's test and logistic regression analysed the data using WHO growth standards. Ethical approval was obtained (KEMRI/SERU/CPHR/002/3525). Results: Wasting: Younger maternal age (18-24 years) presented higher odds of infant wasting across all timepoints: 6 weeks aOR 4.31 (CI: 1.11, 1.83), 6 months aOR 4.49 (CI: 1.09, 27.34), and 12 months aOR 5.49 (CI: 1.41, 32.97). Stunting: At 6 months, infants of underweight mothers and those on second-line antiretroviral therapy (ART) regimens had higher odds of stunting aOR 4.76 (CI: 1.36, 16.65) and aOR 5.49 (CI: 1.64, 18.38), respectively. At 12 months, poor maternal ART adherence aOR 4.11 (CI: 1.14, 14.82) and mothers on second-line ART regimens aOR 3.68 (CI: 1.09, 12.49) had increased odds of infant stunting. Underweight: At 6 weeks, high maternal viral load aOR 6.33 (CI: 2.31, 17.36) was associated with higher odds underweight infants, whereas employed mothers had lower odds of underweight infants at 6 and 12 months aOR 0.10 (CI: 0.03, 0.32) and aOR 0.22 (CI: 0.09, 0.59) respectively. The results highlight maternal nutrition and ART adherence's influence on infant nutritional status and HIV vertical transmission risk. The study recommended integrating comprehensive nutritional care into HIV policies and enhancing ART counselling to reduce vertical transmission risk and poor infant growth.