Although family physicians (FPs) are community-oriented primary care generalists and should be the entry point for the population’s interaction with the health system, they are underrepresented in research on the climate change, migration, and health(care) nexus (hereafter referred to as the nexus). Similarly, FPs can provide valuable insights into building capacity through integrating health-determining sectors for climate-resilient and migration-inclusive health systems, especially in Sub-Saharan Africa (SSA). Here, we explore FPs’ perceptions on the nexus in SSA and on intersectoral capacity building. Three focus groups conducted during the 2019 WONCA-Africa conference in Uganda were transcribed verbatim and analyzed using an inductive thematic approach. Participants’ perceived interactions related to (1) migration and climate change, (2) migration for better health and healthcare, (3) health impacts of climate change and the role of healthcare, and (4) health impacts of migration and the role of healthcare were studied. We coined these complex and reinforcing interactions as continuous feedback loops intertwined with socio-economic, institutional, and demographic context. Participants identified five intersectoral capacity-building opportunities on micro, meso, macro, and supra (international) levels: multi-dimensional and multi-layered governance structures; improving FP training and primary healthcare working conditions; health advocacy in primary healthcare; collaboration between the health sector and civil society; and more responsibilities for high-income countries. This exploratory study presents a unique and novel perspective on the nexus in SSA which contributes to interdisciplinary research agendas and FP policy responses on national, regional, and global levels.