With the rapid increase of microservice architecture and Cloud-native systems, digital transformations have enabled Financial and Enterprise Applications to be developed to be highly scalable, agile, and innovative. The Application Programming Interfaces (API) support communication between the Services, Platforms, and External Stakeholders and are critical to the success of these Distributed Systems. Given the volume of APIs available, the Attack Surface has grown tremendously, therefore leading to the increase in Threats related to API including: Credential Abuse, Data Exfiltration, Distributed Denial of Service, and Advanced Persistent Threats. Traditional perimeter-based security systems and static API management methods are becoming ineffective in Highly Dynamic and Decentralized environments. This study presents a Secure and Intelligent API Governance Framework for Financial and Enterprise Microservices Ecosystems which combines Zero Trust and AI-based Anomaly Detection methods for Adaptive and Proactive API Protection. This Governance Framework includes: Continuous Authentication, Fine-Grained Authorization, Behavioural Analytics, and Real-Time Monitoring. The study utilizes a Conceptual and Analytical approach to develop a Layered Governance Architecture designed to support the Business Objectives, Requirements for Regulatory Compliance, and Operational Resilience of an Organization. The study results have demonstrated that Governance Based on Zero Trust provides improved Threat Detection and Reduces Response Time over the Alternatives.