Mobile Ad hoc Networks (MANETs) is a self‐organizing networks without having a fixed infrastructure for making them susceptible to security threats. Intrusion Detection Systems (IDS) promotes security in MANETs by identifying malicious activities. Leader election is a fundamental aspect of IDS deployment, impacting resource allocation and system efficiency. This article presents a novel approach, the Crossover Boosted Grey Wolf Optimizer (CBGWO), for leader election and resource allocation in MANET‐based IDS. The proposed CBGWO algorithm integrates the Grey Wolf Optimizer (GWO) with innovative crossover operators that have an ability to enhance the capabilities of exploration and exploitation in the optimization process. The leader election problem is solved through applying multi‐objective optimization by considering energy consumption, reputation, and communication overhead. Objective functions are defined to maximize energy efficiency while maintaining a balanced distribution of leadership roles. Extensive simulations are conducted, varying network densities and the percentage of selfish nodes. Results demonstrate the effectiveness of the CBGWO‐based model in balancing energy consumption, prolonging network lifespan, and enhancing intrusion detection by comparing different state‐of‐the‐art models such as PCA‐FELM, CTAA‐MPSO, FLS‐RE, LEACH, DCAIDS, WOA‐GA, and VOELA. The proposed model achieved an energy consumption of 4.31 J, network lifetime of 560.482 ms, and average intrusion detection latency of 0.12 s, respectively. The proposed model outperforms than existing random and connectivity‐based leader election methods that is evaluated by taking main consideration of energy efficiency and network survivability. This research contributes to the field by introducing a robust algorithm for leader election in MANET‐based IDS, addressing challenges posed by network dynamics and resource constraints. The CBGWO‐based approach showcases its potential to achieve effective leader election and efficient resource allocation, thereby enhancing the security and sustainability of MANETs.