Evidence has shown that maternal HIV infection has adverse effects on child birth weight. However, the effect of anti-retroviral therapy (ART) on pregnancy outcome is not conclusive. Ascertaining causality of these associations remain largely unexamined and untested, and if confirmed would help policy makers to improve implementation and sensitization of PMTCT program. However, assessing causal effect has been limited due to ethical concerns if randomized controlled trials are appropriate. We aim to estimate the causal effect of maternal HIV on birth weight and the causal effect of knowledge of HIV status on exclusive breastfeeding while ascertaining the mediating effect of ART using observational data. Data on over 18,000 and 16,000 children still alive and born within five years of the 2010 and 2015-16 Malawi Demographic and Health Surveys were analysed. A set of methods for confounder balance namely, the 1:1 nearest neighbour (NN) matching, matching on the propensity score (PS) and inverse weighting the propensity score (PS) were used. Before matching, place of residence, region, anaemia level and age were statistically different between HIV-infected and HIV-uninfected mothers for both the 2010 and 2015-16 data. After matching, the selected confounding variables were distributed similarly between HIV-infection statuses. Maternal HIV infection had a negative effect on infant birth weight for the 2010 data and had a positive effect on birth weight for the 2015-16 data with p-values <0.001. Uptake of ART did not mediate the effect of HIV infection on birth weight. Maternal knowledge of HIV status was not associated with behaviour concerning exclusive breastfeeding. We have found conflicting evidence on the association between maternal HIV infection and birth weight. The adverse association between maternal HIV infection and child birth weight found for the 2010 data could more likely be causal. However, the increased birth weight among infants born to HIV infected mothers in 2015-16 may show the recent successes of policies and interventions within the PMTCT program in Malawi. However, the purported mediating effect of ART on the association between HIV infection and birth weight was not found. Prenatal care interventions should continue to be supported among ANC clinics in Malawi.