The Internet of Things (IoT) has revolutionized agriculture by optimizing resource usage and enabling real-time field monitoring, but its widespread adoption brings security challenges. The protection of sensitive agricultural data requires robust authentication mechanisms, especially in the face of emerging quantum technologies that may render traditional security methods inadequate. A solution tailored for smart agriculture systems emerges as a lattice-based authentication scheme (LB-SAS). With the leverage of complex mathematical problems like SIS or ISIS, LB-SAS offers resilience against quantum attacks, ensuring the security of IoT-driven agricultural systems. The rigorous security analysis validates LB-SAS’s effectiveness in safeguarding against quantum threats. In summary, as IoT continues to transform agriculture, implementing resilient security measures such as LB-SAS becomes paramount to mitigate risks and maintain the integrity of agricultural operations amid the increasing connectivity of the digital landscape.