ABSTRACT Vulnerable low-income groups were most affected by Zika virus (ZIKV)-related neurologic syndrome during the 2014–2016 outbreak in Brazil. Major ZIKV infection response took place in Primary Health Care (PHC), including prevention strategies and risk communication. We aimed to detect knowledge and beliefs, as well as knowledge gaps among vulnerable women at the PHC level. A cross-sectional study was carried out in two low-income urban community settings: a small municipality with few ZIKV infection cases and a large municipality hard-hit by the epidemic. An open-ended data collection instrument centred on ZIKV infection knowledge, sources of information, possible causes, symptoms, risk perception, consequences for pregnant women and PHC point-of-care communication was developed. Interviews were recorded, transcribed and content coded for thematic analysis. Most of the seventy-nine respondents had some knowledge of the disease, acknowledging the vector as the source of infection and associating microcephaly with the disease, but distanced themselves from possible ZIKV infection and related risk. PHC services in both communities did not adequately communicate risk for women and children. In an uncertain future scenario as to disease re-emergence, awareness may be diminished and acquired knowledge lost, configuring a public health challenge that must be overcome.