Congenital infection with Trypanosoma cruzi remains a major route for Chagas disease transmission in endemic and non-endemic regions. We evaluated an intervention strategy aimed to detect congenital Chagas disease cases at a major hospital in the Ecuadorian Amazon via cord blood analysis at the time of delivery. All women giving birth at the hospital during the study period (191) were invited to participate. Among them, two (1.0%) did not adjust to the inclusion criteria and four (2.1%) declined to participate in the study, showing the intervention had good acceptability among the mothers. It was possible to obtain cord blood samples during 146 of the deliveries, and only one woman was found to be seropositive, without evidence of transmission to the newborn at delivery or 8 months later. In addition, sociodemographic and economic characterization of the study population revealed that few women had previous knowledge about Chagas disease (16.1%) whereas more than half (62.5%) recognized the vector. Recognizing the vector and having seen it indoors were associated with women from rural families, involved in agriculture, and hunting in the forest. Interestingly, most women (87.3%) reported having easy access to Ecuador's national health system, suggesting serological screening during prenatal visits would be of value in this province. With a proper prenatal screening system in place, cord blood screening would allow for timely detection of T. cruzi infection in newborns from both seropositive women and the minority (2.1%) of women who do not comply with prenatal care visits.