This study aimed to assess the impact of the Bolsa Familia Program on perinatal outcomes of pregnant women. A cohort study was conducted with pregnant women supported by prenatal services at 17 Family Health Units in Bahia, Brazil. A previously tested structured questionnaire, which has sociodemographic, economic, prenatal care, lifestyle, and nutritional variables, has been used to collect data. The outcomes included premature birth and low birth weight. A hierarchical conceptual model was constructed, and logistic regression analysis was performed. From a total of 1173 pregnant women, the identified average age was 25.44 years and 34.10% had pre-gestational overweight. The non-beneficiary pregnant women presented a 1.54 (95% CI = 0.46–5.09) times higher chance of giving birth to children with low weight and a 1.03 (95% CI = 95% CI = 0.53–2.00) times chance of premature birth when compared to the beneficiary group. In the multilevel model, some variables were statistically significant, such as age between 18 and 24 years (p = 0.003), age greater than or equal to 35 years (p = 0.025), family income (p = 0.008), employment status (p = 0.010), and maternal height (p = 0.009). The Bolsa Familia Program, as an integrated strategy of social inclusion and economic development, is suggested to exert a protective effect on the health of mother-concept binomial.