While stigmatisation is universal, stigma research in low- and middle-income countries (LMIC) is limited. LMIC stigma research predominantly concerns health-related stigma, primarily regarding HIV/AIDS or mental illness from an adult perspective. While there are commonalities in stigmatisation, there are also contextual differences. The aim of this study in DR Congo (DRC), as a formative part in the development of a common stigma reduction intervention, was to gain insight into the commonalities and differences of stigma drivers (triggers of stigmatisation), facilitators (factors positively or negatively influencing stigmatisation), and manifestations (practices and experiences of stigmatisation) with regard to three populations: unmarried mothers, children formerly associated with armed forces and groups (CAAFAG), and an indigenous population. Group exercises, in which participants reacted to statements and substantiated their reactions, were held with the ‘general population’ (15 exercises, n = 70) and ‘populations experiencing stigma’ (10 exercises, n = 48). Data was transcribed and translated, and coded in Nvivo12. We conducted framework analysis. There were two drivers mentioned across the three populations: perceived danger was the most prominent driver, followed by perceived low value of the population experiencing stigma. There were five shared facilitators, with livelihood and personal benefit the most comparable across the populations. Connection to family or leaders received mixed reactions. If unmarried mothers and CAAFAG were perceived to have taken advice from the general population and changed their stereotyped behaviour this also featured as a facilitator. Stigma manifested itself for the three populations at family, community, leaders and services level, with participation restrictions, differential treatment, anticipated stigma and feelings of scapegoating. Stereotyping was common, with different stereotypes regarding the three populations. Although stigmatisation was persistent, positive interactions between the general population and populations experiencing stigma were shared as well. This study demonstrated utility of a health-related stigma and discrimination framework and a participatory exercise for understanding non-health related stigmatisation. Results are consistent with other studies regarding these populations in other contexts. This study identified commonalities between drivers, facilitators and manifestations—albeit with population-specific factors. Contextual information seems helpful in proposing strategy components for stigma reduction.