The rapid growth of the Internet of Things (IoT) has revolutionized various industries by enabling interconnected devices to exchange data seamlessly. However, IoT systems face significant security challenges due to decentralized architectures, resource-constrained devices, and dynamic network environments. These challenges include denial-of-service (DoS) attacks, anomalous network behaviors, and data manipulation, which threaten the security and reliability of IoT ecosystems. New methods based on machine learning have been reported in the literature, addressing topics such as intrusion detection and prevention. This paper proposes an advanced anomaly detection framework for IoT networks expressed in several phases. In the first phase, data preprocessing is conducted using techniques like the Median-KS Test to remove noise, handle missing values, and balance datasets, ensuring a clean and structured input for subsequent phases. The second phase focuses on optimal feature selection using a Genetic Algorithm enhanced with eagle-inspired search strategies. This approach identifies the most significant features, reduces dimensionality, and enhances computational efficiency without sacrificing accuracy. In the final phase, an ensemble classifier combines the strengths of the Decision Tree, Random Forest, and XGBoost algorithms to achieve the accurate and robust detection of anomalous behaviors. This multi-step methodology ensures adaptability and scalability in handling diverse IoT scenarios. The evaluation results demonstrate the superiority of the proposed framework over existing methods. It achieves a 12.5% improvement in accuracy (98%), a 14% increase in detection rate (95%), a 9.3% reduction in false positive rate (10%), and a 10.8% decrease in false negative rate (5%). These results underscore the framework’s effectiveness, reliability, and scalability for securing real-world IoT networks against evolving cyber threats.