The Internet of Things (IoT) plays a crucial role in enhancing technology by facilitating data transfer, storage, control, and management across networks. Secure communication within IoT environments remains a significant challenge. This research aims to enhance IoT security by integrating Message Queuing Telemetry Transport (MQTT) and MQTT‐Sensor Network (MQTT‐SN) protocols with the Dual Mutation‐Based Seagull Optimization Algorithm (DMBSOA). MQTT, known for its lightweight and dependable messaging, is widely used in the IoT community but is vulnerable to cyber‐attacks, particularly concerning privacy and authentication. DMBSOA, inspired by seagulls' foraging behavior, optimizes MQTT settings to enhance security, reliability, and performance. The proposed model dynamically adjusts key parameters such as transmission frequency, Quality of service (QoS) levels, and message size to improve energy consumption, throughput, end‐to‐end delay, and packet delivery ratio. A comprehensive system model is presented, comprising publisher, subscriber, and broker nodes, with security mechanisms integrated into the broker to ensure data integrity, authentication, and encryption. MQTT operates over Transmission Control Protocol/Internet Protocol (TCP/IP), while MQTT‐SN uses User Datagram Protocol (UDP), catering to resource‐constrained devices and low‐power modes. The proposed technique attained throughput (68 kB), energy consumption (120 mJ), security level (96%), energy efficiency (98.80%), path loss (22 dB), end‐to‐end delay (35 ms), processing time (230 s) and packet delivery ratio (0.98). The DMBSOA‐optimized MQTT protocol demonstrates superior performance compared to these models, highlighting its potential to meet the evolving demands of IoT security. This research underscores the effectiveness of DMBSOA in enhancing MQTT protocol security and efficiency, providing a promising solution for secure IoT communication.