Mozambique implemented in 2021 a formative assessment in 22 prisons to identify the operational and logistical needs for the second round of the Biobehavioral Survey (BBS). Barriers and facilitators that could be anticipated in conducting BBS in prisons, in preparation for implementation, was evaluated using semi-structured questionnaires administered to key informants (directors and other kind of managers staff). The data were cleaned and analyzed using Microsoft Excel, and the categorical variables were summarized by means of simple frequencies and percentages. In most prisons the current prison capacity far exceeds the theoretical capacity, 40.9% have a theoretical capacity of ≥ 50 inmates, 81.8% have inmates who exceed their theoretical capacity. In the country half of the prisons receive only male inmates, and only one female, 54.5% of the prisons visited have inmates under 18 years of age, 72.7% of the prisons had a private space available for the survey, the penitentiary establishments have the physical space for study; ensuring the safety of staff within the facilities; involvement of correctional officers and a clinical focal point. However, barriers such as time management due to prison opening hours, prison laws, restrictions, or permits for research may change without notice due to security, lockdowns, riots, or other situations that may hinder the implementation of research. The implementation of successive and regular rounds of BBS in different environments, contexts and populations constitute opportunities for generating information and indicators not always captured by programmatic data and not only as an opportunity for offering and making healthcare available in prison environments that in a routine context, but these populations normally have also not had equal opportunities. Currently, little is known about the implementation of a BBS in a correctional environment and only a few barriers can be anticipated, for Mozambique’s context, these challenges and obstacles can be overcome through clear communication and collaboration with officials at all levels.