Background Conditional Cash Transfer Programs have been developed in Latin America in response to poverty and marked social inequalities on the continent. In Brazil, the Bolsa Familia Program (BFP) was implemented to alleviate poverty and improve living conditions, health, and education for socioeconomically vulnerable populations. However, the effect of this intervention on maternal and child health is not well understood. Methods We will evaluate the effect of BFP on maternal and child outcomes: 1. Birth weight; 2. Preterm birth; 3. Maternal mortality; and 4. Child growth. Dynamic retrospective cohort data from the 100 Million Brazilian Cohort (2001 to 2015) will be linked to three different databases: Live Birth Information System (2004 to 2015); Mortality Information System (2011 to 2015); and Food and Nutritional Surveillance System (2008 to 2017). The definition of exposure to the BFP varies according to the outcome studied. Those who never received the benefit until the outcome or until the end of the follow-up will be defined as not exposed. The effects of BFP on maternal and child outcomes will be estimated by a combination of propensity score-based methods and weighted logistic regressions. The analyses will be further stratified to reflect changes in the benefit entitlement before and after 2012. Discussion Harnessing a large linked administrative cohort allows us to assess the effect of the BFP on maternal and child health, while considering a wide range of explanatory and confounding variables.