Gender-based violence has been widely used by various actors against the most vulnerable individuals in conflict-affected settings. Internally displaced girls and women are especially susceptible to suffer from this type of violence; nevertheless, they frequently choose not to report it. The present research identifies and analyses the reasons for the under-reporting of gender-based violence occurrences against the above-mentioned individuals in northern Mozambique, namely, the province of Cabo Delgado. In the first phase of primary data collection, the researcher conducted two focus group discussions to obtain a transparent understanding of the community members’ interpretations, including internally displaced people. In a second phase, seventeen semi-structured interviews were conducted with community agents, activists, service providers, international and non-governmental organizations representatives, and political and religious figures. Subsequently, the findings were evaluated through an altered version of the ecological model (What Works to Prevent Violence, 2018). The results revealed that under-reporting of gender-based violence cases is caused by the following reasons: victim’s fear; social stigma; fear of retaliation; lack of information about gender-based violence and respective materialization; culture-blaming; distorted interpretations of female and male identities; the perpetrators’ influence within the community; lack of preparedness of officials working formal institutions, including hospitals, to refer victims to judicial bodies; women empowerment as a secondary subject within decision-making bodies; prevalence and importance of informal institutions and respective decisions; lack of official supervision on informal institutions; grassroots’ lack of knowledge on the creation or amendment of laws; male majority in security forces, including police stations and military; abuse of authority; lack of training of security forces concerning gender-based violence and respective long-term implications; absence of a standardized reporting process; and morosity of the trial. Therefore, this research points out that under-reporting of gender-based violence must be evaluated from a variety of cultural, social, and political perspectives.