Effective digitalization through Port Community Systems (PCS) is essential for improving cargo clearance efficiency, reducing dwell times, and enhancing transparency in port operations. This study examined the effect of Port Community System (PCS) Digitalization, focusing on Level of Automation, Integration of Port Stakeholders, Real-time Data Sharing, and Electronic Documentation & Payments, on the Operational Performance of Cargo Clearance at the Nigerian Ports Authority. Using a descriptive correlational research design, data were collected from 245 key stakeholders across the NPA, Nigeria Customs Service, terminal operators, and freight forwarders via a structured questionnaire. Partial Least Squares Structural Equation Modeling (PLS-SEM) was used for analysis. The findings revealed that Level of Automation (β = 0.342, p = 0.042), Real-time Data Sharing (β = 0.389, p = 0.034), and Electronic Documentation & Payments (β = 0.456, p = 0.011) have a significant positive effect on operational performance, improving cargo dwell time, documentation accuracy, clearance speed, and stakeholder satisfaction. However, Integration of Port Stakeholders (β = 0.298, p = 0.108) showed no significant effect, indicating a gap in collaborative implementation at the NPA. The study concluded that while the transactional and data-sharing elements of PCS are successfully driving efficiency gains, collaborative integration remains a challenge. It is therefore recommended that the NPA should prioritize the acceleration of Electronic Documentation & Payments and Real-time Data Sharing while simultaneously addressing the governance and institutional gaps that currently impede the success of stakeholder integration.