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Coastal areas are particularly sensitive because they are complex, and related land use conflicts are more intense than those in noncoastal areas. In addition to representing a unique encounter of natural and socioeconomic factors, coastal areas have become paradigms of progressive urbanisation and economic development. Our study of the infrastructural mega project of Patimban Seaport in Indonesia explores the factors driving land use changes and the subsequent land use conflicts emerging from large-scale land transformation in the course of seaport development and mega project governance. We utilised interviews and questionnaires to investigate institutional aspects and conflict drivers. Specifically, we retrace and investigate the mechanisms guiding how mega project governance, land use planning, and actual land use interact. Therefore, we observe and analyse where land use conflicts emerge and the roles that a lack of stakeholder interest involvement and tenure-responsive planning take in this process. Our findings reflect how mismanagement and inadequate planning processes lead to market failure, land abandonment and dereliction and how they overburden local communities with the costs of mega projects. Enforcing a stronger coherence between land use planning, participation and land tenure within the land governance process in coastal land use development at all levels and raising the capacity of stakeholders to interfere with governance and planning processes will reduce conflicts and lead to sustainable coastal development in Indonesia.