Malnutrition and infectious disease often coexist in socially inequitable contexts. Malnutrition in the perinatal period adversely affects offspring development and lifelong non-communicable disease risk. Less is known about the effects of infectious disease exposure during critical windows of development and health, and links between in utero HIV-exposure in the absence of neonatal infection, perinatal nutritional environments, and infant development are poorly defined. In a pilot feasibility study at Kalafong Hospital, Pretoria, South Africa, we aimed to better understand relationships between maternal HIV infection and the early nutritional environment of in utero HIV exposed uninfected (HEU) infants. We also undertook exploratory analyses to investigate relationships between food insecurity and infant development. Mother-infant dyads were recruited after delivery and followed until 12 weeks postpartum. Household food insecurity, nutrient intakes and dietary diversity scores did not differ between mothers living with or without HIV. Maternal reports of food insecurity were associated with lower maternal nutrient intakes 12 weeks postpartum, and in infants, higher brain-to-body weight ratio at birth and 12 weeks of age, and attainment of fewer large movement and play activities milestones at 12 weeks of age, irrespective of maternal HIV status. Reports of worry about food runout were associated with increased risk of stunting for HEU, but not unexposed, uninfected infants. Our findings suggest that food insecurity, in a vulnerable population, adversely affects maternal nutritional status and infant development. In utero exposure to HIV may further perpetuate these effects, which has implications for early child development and lifelong human capital.