This study examines the intra-church conflict’s forms, experiences, and patterns within three major Protestant denominations in Tanzania. Adopting a pragmatist philosophy and a qualitatively dominant concurrent mixed-methods design, the study advances a novel theoretical synthesis, the System-Identity Nexus, integrating SST with SIT. Quantitative data from 171 respondents, analysed through partial least squares structural equation modelling, reveal that institutional gaps and identity mobilisation significantly predict conflict prevalence and factionalism, whereas robust electoral design and clear constitutional frameworks act as significant suppressors. Thematic analysis of interviews with eight key informants identified four interconnected conflict ecologies: ritual intimidation, territorial disputes, material and transactional conflicts, and identity factionalism-linked underwater campaigns. The study concludes that ecclesiastical conflict constitutes a chronic, structurally reproduced pathology and proposes a three-pillar reform agenda to strengthen democratic practices, accountability, and inclusive belonging within Tanzanian Protestant churches.