Due to the recent advances in the domain of smart agriculture as a result of integrating traditional agriculture and the latest information technologies including the Internet of Things (IoT), cloud computing, and artificial intelligence (AI), there is an urgent need to address the information security-related issues and challenges in this field. In this article, we propose the integration of lightweight cryptography techniques into the IoT ecosystem for smart agriculture to meet the requirements of resource-constrained IoT devices. Moreover, we investigate the adoption of a lightweight encryption protocol, namely, the Expeditious Cipher (X-cipher), to create a secure channel between the sensing layer and the broker in the Message Queue Telemetry Transport (MQTT) protocol as well as a secure channel between the broker and its subscribers. Our case study focuses on smart irrigation systems, and the MQTT protocol is deployed as the application messaging protocol in these systems. Smart irrigation strives to decrease the misuse of natural resources by enhancing the efficiency of agricultural irrigation. This secure channel is utilized to eliminate the main security threat in precision agriculture by protecting sensors’ published data from eavesdropping and theft, as well as from unauthorized changes to sensitive data that can negatively impact crops’ development. In addition, the secure channel protects the irrigation decisions made by the data analytics (DA) entity regarding the irrigation time and the quantity of water that is returned to actuators from any alteration. Performance evaluation of our chosen lightweight encryption protocol revealed an improvement in terms of power consumption, execution time, and required memory usage when compared with the Advanced Encryption Standard (AES). Moreover, the selected lightweight encryption protocol outperforms the PRESENT lightweight encryption protocol in terms of throughput and memory usage.