Background The COVID-19 pandemic has disproportionately impacted intersectionally marginalised migrants, revealing systemic disparities in health outcomes and vaccine uptake. An in-depth understanding of the underlying social and structural factors influencing health behaviours is necessary to develop tailored interventions for migrants but has been seldom explored. Therefore, this qualitative study aimed to explore the contextual factors shaping COVID-19 vaccination decision-making among Congolese migrants in the UK. Methods A community-based participatory research study was designed and led by a community-academic partnership in London, UK (2021-2022). Peer-led, semi-structured interviews were conducted in Lingala with 32 adult Congolese migrants and explored beliefs, perceptions and lived experiences of migration, healthcare and vaccination and the COVID-19 pandemic. Reflexive thematic analysis generated two themes and a model conceptualising the vaccination decision-making process was developed. Participants and community partners were financially compensated, and the study received ethical approval from the University of London ethics committee (REC: 2021.0128). Findings Participants highlighted the incompatibility of lockdown restrictions with their communal culture, which intensified feelings of exclusion and alienation. They expressed concerns about COVID-19 vaccination safety and effectiveness, partly informed by experiences and legacies of discrimination and exploitation of Black Africans. Inequality in the pandemic response and COVID-19 outcomes heightened participants’ sense that their views and needs were being overlooked; accordingly, government sources and information were perceived as coercive and untrustworthy. Drawing on this data, our model depicts the interplay between institutional trust, belonging, and message perception which shaped participants’ vaccination decisions and led to (non-)engagement with COVID-19 vaccination. Conclusion This research enhances understanding of how social and contextual factors may influence migrants’ engagement with health interventions. It underscores the necessity of partnering with migrant communities to understand their needs in context and co-design tailored interventions and inclusive messaging strategies which foster trust and belonging. Implementing systemic changes to address structural inequalities will be crucial to create an environment that supports engagement with health-protective behaviours and enhances health outcomes among migrant communities.