Zigbee is the standard communication protocol for the Internet of Things (IoT), which has a smaller code size and reduced memory requirements. It is implemented in wireless control systems and applications like home environment control, industrial plant monitoring, and security systems. Its specification has security features to protect against various threats, but it lacks complete end-to-end security, which is necessary in the upcoming applications of the IoT, like smart cities. This paper implemented a system to develop secure applications for Zigbee-based IoT systems, using a widely accepted lightweight security approach of using elliptic curve cryptography on a Cortex-M series microcontroller. It handles both confidentiality and authentication aspects at the network and application layers of Zigbee. Galois Counter Mode is used for encrypting the messages, which helps in preventing attacks due to the properties of XOR and truncation. Zigbee application layer security and link layer key generation, joining, privacy, and authentication attributes are selected. The use of ECC with ARM's Thumb-2 instruction set enables faster computations and smaller code sizes. The ARM architecture security features are implemented alongside the ECC to provide more robust security in the system. This system was designed, developed, and tested for its complete functioning. To conclude, the Zigbee microcontroller-based IoT system developed a secure system that gave application acceptance a boost.