Poor nutrition outcomes among children have become one of the major public health concerns in South Africa, attributed to poor feeding practices and maternal nutrition-related knowledge with conflicting data. In view of this, a cross-sectional study was conducted to determine the association of nutrition outcomes of children aged under two years with feeding practices and maternal nutrition-related knowledge in Mbombela, South Africa. Mothers’ nutrition-related knowledge was estimated using an adapted structured questionnaire on colostrum, continued breastfeeding, diarrhea prevention and treatment using oral rehydration solution, immunization, and family planning, and scored as excellent (80–100), good (60–79), average (40–59), and fair (0–39). This was along with questions on socio-demographic factors and obstetric history, as well as anthropometric measurements. Child nutrition outcomes were estimated by WHO classification using z-scores for stunting (length-for-age (LAZ)), underweight (weight-for-age (WAZ)), and thinness (body mass index-for-age (BAZ)). Using STATA 17, 400 pairs of children (8 ± 6 months) and their mothers (29 ± 6 years) participated in the study and were living in a poor socio-economic status environment. Half of children were stunted (50%) and over half (54%) were obese, while mothers were underweight (39%) and overweight (34%). In addition to one third of mothers reporting obstetric complications, two thirds, initiated breastfeeding within one hour of delivery, 30% exclusively breastfed, 48% introduced early complementary feeding, and 70% practiced mixed feeding. Twenty-eight percent (28%) of mothers had fair nutrition-related knowledge, while 66% had average knowledge, 6% good knowledge, and none of the mothers had excellent knowledge. A chi-square test showed that mothers’ nutrition-related knowledge was significantly associated with child stunting. The final hierarchical logistic regression showed significant associations of stunting with mothers’ nutrition-related knowledge (average: AOR = 1.92, 95%CI: 1.12–3.29), child’s age (6–11 months: AOR = 2.63, 95%CI: 1.53–4.53 and 12–23 months: AOR = 3.19, 95%CI: 1.41–7.25), and education (completing Grade 12: AOR = 0.36, 95%CI: 0.15–0.86). Contextual and intensified interventions on continued education for mothers to gain accurate information on nutrition-related knowledge and feeding practices could ultimately enhance child nutrition outcomes in poorer settings. Efforts should therefore be made to ensure that nutrition knowledge is appropriately provided based on the phases of child growth from 0 to 2 years, even beyond infancy into school age.